getrelabundcommand.cpp

   1 /*
   2  *  getrelabundcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 6/21/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getrelabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> GetRelAbundCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"groups","label","scale","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "GetRelAbundCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 GetRelAbundCommand::GetRelAbundCommand(){
  26         try {
  27                 abort = true;
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["relabund"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> GetRelAbundCommand::getRequiredParameters(){
  39         try {
  40                 vector<string> myArray;
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "GetRelAbundCommand", "getRequiredParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 vector<string> GetRelAbundCommand::getRequiredFiles(){
  50         try {
  51                 string Array[] =  {"shared"};
  52                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "GetRelAbundCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 GetRelAbundCommand::GetRelAbundCommand(string option) {
  62         try {
  63                 globaldata = GlobalData::getInstance();
  64                 abort = false;
  65                 allLines = 1;
  66                 labels.clear();
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string AlignArray[] =  {"groups","label","scale","outputdir","inputdir"};
  74                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string,string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //initialize outputTypes
  87                         vector<string> tempOutNames;
  88                         outputTypes["relabund"] = tempOutNames;
  89
  90                         //if the user changes the output directory command factory will send this info to us in the output parameter
  91                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  92                                 outputDir = "";
  93                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  94                         }
  95
  96                         //make sure the user has already run the read.otu command
  97                         if ((globaldata->getSharedFile() == "")) {
  98                                  m->mothurOut("You must read a list and a group, or a shared file before you can use the get.relabund command."); m->mothurOutEndLine(); abort = true;
  99                         }
 100
 101                         //check for optional parameter and set defaults
 102                         // ...at some point should added some additional type checking...
 103                         label = validParameter.validFile(parameters, "label", false);
 104                         if (label == "not found") { label = ""; }
 105                         else {
 106                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 107                                 else { allLines = 1;  }
 108                         }
 109
 110                         //if the user has not specified any labels use the ones from read.otu
 111                         if (label == "") {
 112                                 allLines = globaldata->allLines;
 113                                 labels = globaldata->labels;
 114                         }
 115
 116                         groups = validParameter.validFile(parameters, "groups", false);
 117                         if (groups == "not found") { groups = ""; pickedGroups = false; }
 118                         else {
 119                                 pickedGroups = true;
 120                                 m->splitAtDash(groups, Groups);
 121                                 globaldata->Groups = Groups;
 122                         }
 123
 124                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "totalgroup"; }
 125
 126                         if ((scale != "totalgroup") && (scale != "totalotu") && (scale != "averagegroup") && (scale != "averageotu")) {
 127                                 m->mothurOut(scale + " is not a valid scaling option for the get.relabund command. Choices are totalgroup, totalotu, averagegroup, averageotu."); m->mothurOutEndLine(); abort = true;
 128                         }
 129                 }
 130
 131         }
 132         catch(exception& e) {
 133                 m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
 134                 exit(1);
 135         }
 136 }
 137
 138 //**********************************************************************************************************************
 139
 140 void GetRelAbundCommand::help(){
 141         try {
 142                 m->mothurOut("The get.relabund command can only be executed after a successful read.otu command of a list and group or shared file.\n");
 143                 m->mothurOut("The get.relabund command parameters are groups, scale and label.  No parameters are required.\n");
 144                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
 145                 m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
 146                 m->mothurOut("The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n");
 147                 m->mothurOut("The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n");
 148                 m->mothurOut("Example get.relabund(groups=A-B-C, scale=averagegroup).\n");
 149                 m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
 150                 m->mothurOut("The get.relabund command outputs a .relabund file.\n");
 151                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 152
 153         }
 154         catch(exception& e) {
 155                 m->errorOut(e, "GetRelAbundCommand", "help");
 156                 exit(1);
 157         }
 158 }
 159
 160 //**********************************************************************************************************************
 161
 162 GetRelAbundCommand::~GetRelAbundCommand(){
 163 }
 164
 165 //**********************************************************************************************************************
 166
 167 int GetRelAbundCommand::execute(){
 168         try {
 169
 170                 if (abort == true) { return 0; }
 171
 172                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "relabund";
 173                 ofstream out;
 174                 m->openOutputFile(outputFileName, out);
 175                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 176
 177                 read = new ReadOTUFile(globaldata->inputFileName);
 178                 read->read(&*globaldata);
 179                 input = globaldata->ginput;
 180                 lookup = input->getSharedRAbundVectors();
 181                 string lastLabel = lookup[0]->getLabel();
 182
 183                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 184                 set<string> processedLabels;
 185                 set<string> userLabels = labels;
 186
 187                 //as long as you are not at the end of the file or done wih the lines you want
 188                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 189
 190                         if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
 191
 192                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 193
 194                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 195                                 getRelAbundance(lookup, out);
 196
 197                                 processedLabels.insert(lookup[0]->getLabel());
 198                                 userLabels.erase(lookup[0]->getLabel());
 199                         }
 200
 201                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 202                                 string saveLabel = lookup[0]->getLabel();
 203
 204                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 205                                 lookup = input->getSharedRAbundVectors(lastLabel);
 206                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 207
 208                                 getRelAbundance(lookup, out);
 209
 210                                 processedLabels.insert(lookup[0]->getLabel());
 211                                 userLabels.erase(lookup[0]->getLabel());
 212
 213                                 //restore real lastlabel to save below
 214                                 lookup[0]->setLabel(saveLabel);
 215                         }
 216
 217                         lastLabel = lookup[0]->getLabel();
 218                         //prevent memory leak
 219                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 220
 221                         if (m->control_pressed) {  outputTypes.clear();  globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
 222
 223                         //get next line to process
 224                         lookup = input->getSharedRAbundVectors();
 225                 }
 226
 227                 if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str());  return 0; }
 228
 229                 //output error messages about any remaining user labels
 230                 set<string>::iterator it;
 231                 bool needToRun = false;
 232                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 233                         m->mothurOut("Your file does not include the label " + *it);
 234                         if (processedLabels.count(lastLabel) != 1) {
 235                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 236                                 needToRun = true;
 237                         }else {
 238                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 239                         }
 240                 }
 241
 242                 //run last label if you need to
 243                 if (needToRun == true)  {
 244                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 245                         lookup = input->getSharedRAbundVectors(lastLabel);
 246
 247                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 248
 249                         getRelAbundance(lookup, out);
 250
 251                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 252                 }
 253
 254                 //reset groups parameter
 255                 globaldata->Groups.clear();
 256                 delete input; globaldata->ginput = NULL;
 257                 delete read;
 258                 out.close();
 259
 260                 if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
 261
 262                 m->mothurOutEndLine();
 263                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 264                 m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
 265                 m->mothurOutEndLine();
 266
 267                 return 0;
 268         }
 269         catch(exception& e) {
 270                 m->errorOut(e, "GetRelAbundCommand", "execute");
 271                 exit(1);
 272         }
 273 }
 274 //**********************************************************************************************************************
 275
 276 int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
 277         try {
 278                 if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
 279
 280
 281                  for (int i = 0; i < thisLookUp.size(); i++) {
 282                         out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
 283
 284                         for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
 285
 286                                 if (m->control_pressed) { return 0; }
 287
 288                                 int abund = thisLookUp[i]->getAbundance(j);
 289
 290                                 float relabund = 0.0;
 291
 292                                 if (scale == "totalgroup") {
 293                                         relabund = abund / (float) thisLookUp[i]->getNumSeqs();
 294                                 }else if (scale == "totalotu") {
 295                                         //calc the total in this otu
 296                                         int totalOtu = 0;
 297                                         for (int l = 0; l < thisLookUp.size(); l++) {  totalOtu += thisLookUp[l]->getAbundance(j); }
 298                                         relabund = abund / (float) totalOtu;
 299                                 }else if (scale == "averagegroup") {
 300                                         relabund = abund / (float) (thisLookUp[i]->getNumSeqs() / (float) thisLookUp[i]->getNumBins());
 301                                 }else if (scale == "averageotu") {
 302                                         //calc the total in this otu
 303                                         int totalOtu = 0;
 304                                         for (int l = 0; l < thisLookUp.size(); l++) {  totalOtu += thisLookUp[l]->getAbundance(j); }
 305                                         float averageOtu = totalOtu / (float) thisLookUp.size();
 306
 307                                         relabund = abund / (float) averageOtu;
 308                                 }else{ m->mothurOut(scale + " is not a valid scaling option."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
 309
 310                                 out << relabund << '\t';
 311                         }
 312                         out << endl;
 313                  }
 314
 315                  return 0;
 316         }
 317         catch(exception& e) {
 318                 m->errorOut(e, "GetRelAbundCommand", "getRelAbundance");
 319                 exit(1);
 320         }
 321 }
 322 //**********************************************************************************************************************
 323 int GetRelAbundCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 324         try {
 325
 326                 vector<SharedRAbundVector*> newLookup;
 327                 for (int i = 0; i < thislookup.size(); i++) {
 328                         SharedRAbundVector* temp = new SharedRAbundVector();
 329                         temp->setLabel(thislookup[i]->getLabel());
 330                         temp->setGroup(thislookup[i]->getGroup());
 331                         newLookup.push_back(temp);
 332                 }
 333
 334                 //for each bin
 335                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 336                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 337
 338                         //look at each sharedRabund and make sure they are not all zero
 339                         bool allZero = true;
 340                         for (int j = 0; j < thislookup.size(); j++) {
 341                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 342                         }
 343
 344                         //if they are not all zero add this bin
 345                         if (!allZero) {
 346                                 for (int j = 0; j < thislookup.size(); j++) {
 347                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 348                                 }
 349                         }
 350                 }
 351
 352                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 353
 354                 thislookup = newLookup;
 355
 356                 return 0;
 357
 358         }
 359         catch(exception& e) {
 360                 m->errorOut(e, "GetRelAbundCommand", "eliminateZeroOTUS");
 361                 exit(1);
 362         }
 363 }
 364
 365 //**********************************************************************************************************************
 366
 367