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