rarefactcommand.cpp

   1 /*
   2  *  rarefactcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactcommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "nseqs.h"
  14 #include "chao1.h"
  15 #include "bootstrap.h"
  16 #include "simpson.h"
  17 #include "simpsoneven.h"
  18 #include "heip.h"
  19 #include "smithwilson.h"
  20 #include "invsimpson.h"
  21 #include "npshannon.h"
  22 #include "shannoneven.h"
  23 #include "shannon.h"
  24 #include "jackknife.h"
  25 #include "coverage.h"
  26
  27 //**********************************************************************************************************************
  28
  29
  30 RareFactCommand::RareFactCommand(string option)  {
  31         try {
  32                 globaldata = GlobalData::getInstance();
  33                 abort = false;
  34                 allLines = 1;
  35                 labels.clear();
  36                 Estimators.clear();
  37
  38                 //allow user to run help
  39                 if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
  40
  41                 else {
  42                         //valid paramters for this command
  43                         string Array[] =  {"iters","freq","label","calc","abund","outputdir","inputdir"};
  44                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  45
  46                         OptionParser parser(option);
  47                         map<string,string> parameters = parser.getParameters();
  48
  49                         ValidParameters validParameter;
  50
  51                         //check to make sure all parameters are valid for command
  52                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  53                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  54                         }
  55
  56                         //if the user changes the output directory command factory will send this info to us in the output parameter
  57                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  58                                 outputDir = "";
  59                                 outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  60                         }
  61
  62                         //make sure the user has already run the read.otu command
  63                         if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the rarefact.single command."); m->mothurOutEndLine(); abort = true; }
  64
  65                         //check for optional parameter and set defaults
  66                         // ...at some point should added some additional type checking...
  67                         label = validParameter.validFile(parameters, "label", false);
  68                         if (label == "not found") { label = ""; }
  69                         else {
  70                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  71                                 else { allLines = 1;  }
  72                         }
  73
  74                         //if the user has not specified any labels use the ones from read.otu
  75                         if(label == "") {
  76                                 allLines = globaldata->allLines;
  77                                 labels = globaldata->labels;
  78                         }
  79
  80                         calc = validParameter.validFile(parameters, "calc", false);
  81                         if (calc == "not found") { calc = "sobs";  }
  82                         else {
  83                                  if (calc == "default")  {  calc = "sobs";  }
  84                         }
  85                         splitAtDash(calc, Estimators);
  86
  87                         string temp;
  88                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
  89                         convert(temp, freq);
  90
  91                         temp = validParameter.validFile(parameters, "abund", false);                    if (temp == "not found") { temp = "10"; }
  92                         convert(temp, abund);
  93
  94                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
  95                         convert(temp, nIters);
  96                 }
  97
  98         }
  99         catch(exception& e) {
 100                 m->errorOut(e, "RareFactCommand", "RareFactCommand");
 101                 exit(1);
 102         }
 103 }
 104 //**********************************************************************************************************************
 105
 106 void RareFactCommand::help(){
 107         try {
 108                 m->mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
 109                 m->mothurOut("The rarefaction.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
 110                 m->mothurOut("The rarefaction.single command parameters are label, iters, freq, calc and abund.  No parameters are required. \n");
 111                 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");
 112                 m->mothurOut("The rarefaction.single command should be in the following format: \n");
 113                 m->mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
 114                 m->mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
 115                 m->mothurOut("The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n");
 116                 validCalculator->printCalc("rarefaction", cout);
 117                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 118                 m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
 119         }
 120         catch(exception& e) {
 121                 m->errorOut(e, "RareFactCommand", "help");
 122                 exit(1);
 123         }
 124 }
 125
 126 //**********************************************************************************************************************
 127
 128 RareFactCommand::~RareFactCommand(){}
 129
 130 //**********************************************************************************************************************
 131
 132 int RareFactCommand::execute(){
 133         try {
 134
 135                 if (abort == true) { return 0; }
 136
 137                 vector<string> outputNames;
 138
 139                 string hadShared = "";
 140                 if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
 141                 else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
 142
 143                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 144
 145                 for (int p = 0; p < inputFileNames.size(); p++) {
 146
 147                         string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
 148                         globaldata->inputFileName = inputFileNames[p];
 149
 150                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 151
 152                         if (inputFileNames.size() > 1) {
 153                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 154                         }
 155                         int i;
 156                         validCalculator = new ValidCalculators();
 157
 158
 159                         for (i=0; i<Estimators.size(); i++) {
 160                                 if (validCalculator->isValidCalculator("rarefaction", Estimators[i]) == true) {
 161                                         if (Estimators[i] == "sobs") {
 162                                                 rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
 163                                                 outputNames.push_back(fileNameRoot+"rarefaction");
 164                                         }else if (Estimators[i] == "chao") {
 165                                                 rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
 166                                                 outputNames.push_back(fileNameRoot+"r_chao");
 167                                         }else if (Estimators[i] == "ace") {
 168                                                 if(abund < 5)
 169                                                         abund = 10;
 170                                                 rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
 171                                                 outputNames.push_back(fileNameRoot+"r_ace");
 172                                         }else if (Estimators[i] == "jack") {
 173                                                 rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
 174                                                 outputNames.push_back(fileNameRoot+"r_jack");
 175                                         }else if (Estimators[i] == "shannon") {
 176                                                 rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
 177                                                 outputNames.push_back(fileNameRoot+"r_shannon");
 178                                         }else if (Estimators[i] == "shannoneven") {
 179                                                 rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
 180                                                 outputNames.push_back(fileNameRoot+"r_shannoneven");
 181                                         }else if (Estimators[i] == "heip") {
 182                                                 rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
 183                                                 outputNames.push_back(fileNameRoot+"r_heip");
 184                                         }else if (Estimators[i] == "smithwilson") {
 185                                                 rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
 186                                                 outputNames.push_back(fileNameRoot+"r_smithwilson");
 187                                         }else if (Estimators[i] == "npshannon") {
 188                                                 rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
 189                                                 outputNames.push_back(fileNameRoot+"r_npshannon");
 190                                         }else if (Estimators[i] == "simpson") {
 191                                                 rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
 192                                                 outputNames.push_back(fileNameRoot+"r_simpson");
 193                                         }else if (Estimators[i] == "simpsoneven") {
 194                                                 rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
 195                                                 outputNames.push_back(fileNameRoot+"r_simpsoneven");
 196                                         }else if (Estimators[i] == "invsimpson") {
 197                                                 rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
 198                                                 outputNames.push_back(fileNameRoot+"r_invsimpson");
 199                                         }else if (Estimators[i] == "bootstrap") {
 200                                                 rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
 201                                                 outputNames.push_back(fileNameRoot+"r_bootstrap");
 202                                         }else if (Estimators[i] == "coverage") {
 203                                                 rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
 204                                                 outputNames.push_back(fileNameRoot+"r_coverage");
 205                                         }else if (Estimators[i] == "nseqs") {
 206                                                 rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
 207                                                 outputNames.push_back(fileNameRoot+"r_nseqs");
 208                                         }
 209                                 }
 210                         }
 211
 212
 213                         //if the users entered no valid calculators don't execute command
 214                         if (rDisplays.size() == 0) { for(int i=0;i<rDisplays.size();i++){       delete rDisplays[i];    } delete validCalculator; return 0; }
 215
 216                         read = new ReadOTUFile(globaldata->inputFileName);
 217                         read->read(&*globaldata);
 218
 219                         order = globaldata->gorder;
 220                         string lastLabel = order->getLabel();
 221                         input = globaldata->ginput;
 222
 223                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 224                         set<string> processedLabels;
 225                         set<string> userLabels = labels;
 226
 227                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 228
 229                         //as long as you are not at the end of the file or done wih the lines you want
 230                         while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 231
 232                                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 233
 234
 235                                 if(allLines == 1 || labels.count(order->getLabel()) == 1){
 236
 237                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 238                                         rCurve = new Rarefact(order, rDisplays);
 239                                         rCurve->getCurve(freq, nIters);
 240                                         delete rCurve;
 241
 242                                         processedLabels.insert(order->getLabel());
 243                                         userLabels.erase(order->getLabel());
 244                                 }
 245
 246                                 if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 247                                         string saveLabel = order->getLabel();
 248
 249                                         delete order;
 250                                         order = (input->getOrderVector(lastLabel));
 251
 252                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 253                                         rCurve = new Rarefact(order, rDisplays);
 254                                         rCurve->getCurve(freq, nIters);
 255                                         delete rCurve;
 256
 257                                         processedLabels.insert(order->getLabel());
 258                                         userLabels.erase(order->getLabel());
 259
 260                                         //restore real lastlabel to save below
 261                                         order->setLabel(saveLabel);
 262                                 }
 263
 264                                 lastLabel = order->getLabel();
 265
 266                                 delete order;
 267                                 order = (input->getOrderVector());
 268                         }
 269
 270                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }  return 0; }
 271
 272                         //output error messages about any remaining user labels
 273                         set<string>::iterator it;
 274                         bool needToRun = false;
 275                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 276                                 m->mothurOut("Your file does not include the label " + *it);
 277                                 if (processedLabels.count(lastLabel) != 1) {
 278                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 279                                         needToRun = true;
 280                                 }else {
 281                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 282                                 }
 283                         }
 284
 285                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    } delete validCalculator; delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 286
 287                         //run last label if you need to
 288                         if (needToRun == true)  {
 289                                 if (order != NULL) {    delete order;   }
 290                                 order = (input->getOrderVector(lastLabel));
 291
 292                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 293                                 rCurve = new Rarefact(order, rDisplays);
 294                                 rCurve->getCurve(freq, nIters);
 295                                 delete rCurve;
 296
 297                                 delete order;
 298                         }
 299
 300
 301                         for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 302                         rDisplays.clear();
 303                         globaldata->gorder = NULL;
 304                         delete input;  globaldata->ginput = NULL;
 305                         delete read;
 306                         delete validCalculator;
 307
 308                 }
 309
 310                 if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 311
 312                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } return 0; }
 313
 314                 m->mothurOutEndLine();
 315                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 316                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 317                 m->mothurOutEndLine();
 318
 319                 return 0;
 320         }
 321         catch(exception& e) {
 322                 m->errorOut(e, "RareFactCommand", "execute");
 323                 exit(1);
 324         }
 325 }
 326 //**********************************************************************************************************************
 327 vector<string> RareFactCommand::parseSharedFile(string filename) {
 328         try {
 329                 vector<string> filenames;
 330
 331                 map<string, ofstream*> filehandles;
 332                 map<string, ofstream*>::iterator it3;
 333
 334
 335                 //read first line
 336                 read = new ReadOTUFile(filename);
 337                 read->read(&*globaldata);
 338
 339                 input = globaldata->ginput;
 340                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 341
 342                 string sharedFileRoot = getRootName(filename);
 343
 344                 //clears file before we start to write to it below
 345                 for (int i=0; i<lookup.size(); i++) {
 346                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 347                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 348                 }
 349
 350                 ofstream* temp;
 351                 for (int i=0; i<lookup.size(); i++) {
 352                         temp = new ofstream;
 353                         filehandles[lookup[i]->getGroup()] = temp;
 354                         groups.push_back(lookup[i]->getGroup());
 355                 }
 356
 357                 while(lookup[0] != NULL) {
 358
 359                         for (int i = 0; i < lookup.size(); i++) {
 360                                 RAbundVector rav = lookup[i]->getRAbundVector();
 361                                 openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 362                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 363                                 (*(filehandles[lookup[i]->getGroup()])).close();
 364                         }
 365
 366                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 367                         lookup = input->getSharedRAbundVectors();
 368                 }
 369
 370                 //free memory
 371                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 372                         delete it3->second;
 373                 }
 374                 delete read;
 375                 delete input;
 376                 globaldata->ginput = NULL;
 377
 378                 return filenames;
 379         }
 380         catch(exception& e) {
 381                 m->errorOut(e, "RareFactCommand", "parseSharedFile");
 382                 exit(1);
 383         }
 384 }
 385 //**********************************************************************************************************************
 386
 387
 388