rarefactsharedcommand.cpp

   1 /*
   2  *  rarefactsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactsharedcommand.h"
  11 #include "sharedsobs.h"
  12 #include "sharednseqs.h"
  13
  14 //**********************************************************************************************************************
  15 vector<string> RareFactSharedCommand::getValidParameters(){
  16         try {
  17                 string Array[] =  {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "RareFactSharedCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 RareFactSharedCommand::RareFactSharedCommand(){
  28         try {
  29                 abort = true;
  30                 //initialize outputTypes
  31                 vector<string> tempOutNames;
  32                 outputTypes["sharedrarefaction"] = tempOutNames;
  33                 outputTypes["sharedr_nseqs"] = tempOutNames;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 vector<string> RareFactSharedCommand::getRequiredParameters(){
  42         try {
  43                 vector<string> myArray;
  44                 return myArray;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "RareFactSharedCommand", "getRequiredParameters");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 vector<string> RareFactSharedCommand::getRequiredFiles(){
  53         try {
  54                 string Array[] =  {"shared"};
  55                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  56                 return myArray;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "RareFactSharedCommand", "getRequiredFiles");
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64
  65 RareFactSharedCommand::RareFactSharedCommand(string option)  {
  66         try {
  67                 globaldata = GlobalData::getInstance();
  68
  69                 abort = false;
  70                 allLines = 1;
  71                 labels.clear();
  72                 Estimators.clear();
  73                 Groups.clear();
  74
  75                 //allow user to run help
  76                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  77
  78                 else {
  79                         //valid paramters for this command
  80                         string Array[] =  {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
  81                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  82
  83                         OptionParser parser(option);
  84                         map<string,string> parameters = parser.getParameters();
  85
  86                         ValidParameters validParameter;
  87
  88                         //check to make sure all parameters are valid for command
  89                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  90                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  91                         }
  92
  93                         //initialize outputTypes
  94                         vector<string> tempOutNames;
  95                         outputTypes["sharedrarefaction"] = tempOutNames;
  96                         outputTypes["sharedr_nseqs"] = tempOutNames;
  97
  98                         //make sure the user has already run the read.otu command
  99                         if (globaldata->getSharedFile() == "") {
 100                                 if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); m->mothurOutEndLine(); abort = true; }
 101                                 else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); m->mothurOutEndLine(); abort = true; }
 102                         }
 103
 104                         //if the user changes the output directory command factory will send this info to us in the output parameter
 105                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 106                                 outputDir = "";
 107                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 108                         }
 109
 110
 111                         //check for optional parameter and set defaults
 112                         // ...at some point should added some additional type checking...
 113                         label = validParameter.validFile(parameters, "label", false);
 114                         if (label == "not found") { label = ""; }
 115                         else {
 116                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 117                                 else { allLines = 1;  }
 118                         }
 119
 120                         //if the user has not specified any labels use the ones from read.otu
 121                         if(label == "") {
 122                                 allLines = globaldata->allLines;
 123                                 labels = globaldata->labels;
 124                         }
 125
 126                         calc = validParameter.validFile(parameters, "calc", false);
 127                         if (calc == "not found") { calc = "sharedobserved";  }
 128                         else {
 129                                  if (calc == "default")  {  calc = "sharedobserved";  }
 130                         }
 131                         m->splitAtDash(calc, Estimators);
 132
 133                         groups = validParameter.validFile(parameters, "groups", false);
 134                         if (groups == "not found") { groups = ""; }
 135                         else {
 136                                 m->splitAtDash(groups, Groups);
 137                         }
 138                         globaldata->Groups = Groups;
 139
 140                         string temp;
 141                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 142                         convert(temp, freq);
 143
 144                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
 145                         convert(temp, nIters);
 146
 147                         temp = validParameter.validFile(parameters, "jumble", false);                   if (temp == "not found") { temp = "T"; }
 148                         if (m->isTrue(temp)) { jumble = true; }
 149                         else { jumble = false; }
 150                         globaldata->jumble = jumble;
 151
 152                         if (abort == false) {
 153
 154                                 string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
 155 //                              format = globaldata->getFormat();
 156
 157
 158                                 validCalculator = new ValidCalculators();
 159
 160                                 for (int i=0; i<Estimators.size(); i++) {
 161                                         if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
 162                                                 if (Estimators[i] == "sharedobserved") {
 163                                                         rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
 164                                                         outputNames.push_back(fileNameRoot+"shared.rarefaction"); outputTypes["sharedrarefaction"].push_back(fileNameRoot+"shared.rarefaction");
 165                                                 }else if (Estimators[i] == "sharednseqs") {
 166                                                         rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
 167                                                         outputNames.push_back(fileNameRoot+"shared.r_nseqs"); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+"shared.r_nseqs");
 168                                                 }
 169                                         }
 170                                 }
 171                         }
 172
 173                 }
 174
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
 178                 exit(1);
 179         }
 180 }
 181
 182 //**********************************************************************************************************************
 183
 184 void RareFactSharedCommand::help(){
 185         try {
 186                 m->mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n");
 187                 m->mothurOut("The rarefaction.shared command parameters are label, iters, groups, jumble and calc.  No parameters are required.\n");
 188                 m->mothurOut("The rarefaction command should be in the following format: \n");
 189                 m->mothurOut("rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n");
 190                 m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
 191                 m->mothurOut("Example rarefaction.shared(label=unique-0.01-0.03,  iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
 192                 m->mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n");
 193                 m->mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");
 194                 validCalculator->printCalc("sharedrarefaction", cout);
 195                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 196                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");
 197                 m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
 198         }
 199         catch(exception& e) {
 200                 m->errorOut(e, "RareFactSharedCommand", "help");
 201                 exit(1);
 202         }
 203 }
 204
 205 //**********************************************************************************************************************
 206
 207 RareFactSharedCommand::~RareFactSharedCommand(){
 208         if (abort == false) {
 209                 delete input;   globaldata->ginput = NULL;
 210                 delete read;
 211                 delete validCalculator;
 212         }
 213 }
 214
 215 //**********************************************************************************************************************
 216
 217 int RareFactSharedCommand::execute(){
 218         try {
 219
 220                 if (abort == true) { return 0; }
 221
 222                 //if the users entered no valid calculators don't execute command
 223                 if (rDisplays.size() == 0) { return 0; }
 224
 225                 read = new ReadOTUFile(globaldata->inputFileName);
 226                 read->read(&*globaldata);
 227
 228                 input = globaldata->ginput;
 229                 lookup = input->getSharedRAbundVectors();
 230                 string lastLabel = lookup[0]->getLabel();
 231
 232                 if (m->control_pressed) {
 233                         globaldata->Groups.clear();
 234                         for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 235                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
 236                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 237                         return 0;
 238                 }
 239
 240
 241                 if (lookup.size() < 2) {
 242                         m->mothurOut("I cannot run the command without at least 2 valid groups.");
 243                         for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
 244                         return 0;
 245                 }
 246
 247                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 248                 set<string> processedLabels;
 249                 set<string> userLabels = labels;
 250
 251                 //as long as you are not at the end of the file or done wih the lines you want
 252                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 253                         if (m->control_pressed) {
 254                                 globaldata->Groups.clear();
 255                                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 256                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
 257                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 258                                 return 0;
 259                         }
 260
 261                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 262                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 263                                 rCurve = new Rarefact(lookup, rDisplays);
 264                                 rCurve->getSharedCurve(freq, nIters);
 265                                 delete rCurve;
 266
 267                                 processedLabels.insert(lookup[0]->getLabel());
 268                                 userLabels.erase(lookup[0]->getLabel());
 269                         }
 270
 271                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 272                                         string saveLabel = lookup[0]->getLabel();
 273
 274                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 275                                         lookup = input->getSharedRAbundVectors(lastLabel);
 276
 277                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 278                                         rCurve = new Rarefact(lookup, rDisplays);
 279                                         rCurve->getSharedCurve(freq, nIters);
 280                                         delete rCurve;
 281
 282                                         processedLabels.insert(lookup[0]->getLabel());
 283                                         userLabels.erase(lookup[0]->getLabel());
 284
 285                                         //restore real lastlabel to save below
 286                                         lookup[0]->setLabel(saveLabel);
 287                         }
 288
 289
 290                         lastLabel = lookup[0]->getLabel();
 291
 292                         //get next line to process
 293                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 294                         lookup = input->getSharedRAbundVectors();
 295                 }
 296
 297                 if (m->control_pressed) {
 298                                 globaldata->Groups.clear();
 299                                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 300                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
 301                                 return 0;
 302                 }
 303
 304                 //output error messages about any remaining user labels
 305                 set<string>::iterator it;
 306                 bool needToRun = false;
 307                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 308                         m->mothurOut("Your file does not include the label " + *it);
 309                         if (processedLabels.count(lastLabel) != 1) {
 310                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 311                                 needToRun = true;
 312                         }else {
 313                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 314                         }
 315                 }
 316
 317                 if (m->control_pressed) {
 318                                 globaldata->Groups.clear();
 319                                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 320                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
 321                                 return 0;
 322                 }
 323
 324                 //run last label if you need to
 325                 if (needToRun == true)  {
 326                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 327                         lookup = input->getSharedRAbundVectors(lastLabel);
 328
 329                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 330                         rCurve = new Rarefact(lookup, rDisplays);
 331                         rCurve->getSharedCurve(freq, nIters);
 332                         delete rCurve;
 333                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 334                 }
 335
 336                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 337
 338                 //reset groups parameter
 339                 globaldata->Groups.clear();
 340
 341                 if (m->control_pressed) {
 342                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }
 343                                 return 0;
 344                 }
 345
 346                 m->mothurOutEndLine();
 347                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 348                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 349                 m->mothurOutEndLine();
 350
 351                 return 0;
 352         }
 353         catch(exception& e) {
 354                 m->errorOut(e, "RareFactSharedCommand", "execute");
 355                 exit(1);
 356         }
 357 }
 358
 359
 360 //**********************************************************************************************************************