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 vector<string> RareFactCommand::getValidParameters(){
  29         try {
  30                 string Array[] =  {"iters","freq","label","calc","abund","processors","outputdir","inputdir"};
  31                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  32                 return myArray;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "RareFactCommand", "getValidParameters");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 vector<string> RareFactCommand::getRequiredParameters(){
  41         try {
  42                 vector<string> myArray;
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "RareFactCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> RareFactCommand::getRequiredFiles(){
  52         try {
  53                 string AlignArray[] =  {"shared","list","rabund","sabund","or"};
  54                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  55                 return myArray;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "RareFactCommand", "getRequiredFiles");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 RareFactCommand::RareFactCommand(){
  64         try {
  65                 abort = true;
  66                 //initialize outputTypes
  67                 vector<string> tempOutNames;
  68                 outputTypes["rarefaction"] = tempOutNames;
  69                 outputTypes["r_chao"] = tempOutNames;
  70                 outputTypes["r_ace"] = tempOutNames;
  71                 outputTypes["r_jack"] = tempOutNames;
  72                 outputTypes["r_shannon"] = tempOutNames;
  73                 outputTypes["r_shannoneven"] = tempOutNames;
  74                 outputTypes["r_heip"] = tempOutNames;
  75                 outputTypes["r_smithwilson"] = tempOutNames;
  76                 outputTypes["r_npshannon"] = tempOutNames;
  77                 outputTypes["r_simpson"] = tempOutNames;
  78                 outputTypes["r_simpsoneven"] = tempOutNames;
  79                 outputTypes["r_invsimpson"] = tempOutNames;
  80                 outputTypes["r_bootstrap"] = tempOutNames;
  81                 outputTypes["r_coverage"] = tempOutNames;
  82                 outputTypes["r_nseqs"] = tempOutNames;
  83         }
  84         catch(exception& e) {
  85                 m->errorOut(e, "RareFactCommand", "RareFactCommand");
  86                 exit(1);
  87         }
  88 }
  89 //**********************************************************************************************************************
  90 RareFactCommand::RareFactCommand(string option)  {
  91         try {
  92                 globaldata = GlobalData::getInstance();
  93                 abort = false;
  94                 allLines = 1;
  95                 labels.clear();
  96                 Estimators.clear();
  97
  98                 //allow user to run help
  99                 if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
 100
 101                 else {
 102                         //valid paramters for this command
 103                         string Array[] =  {"iters","freq","label","calc","abund","processors","outputdir","inputdir"};
 104                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 105
 106                         OptionParser parser(option);
 107                         map<string,string> parameters = parser.getParameters();
 108
 109                         ValidParameters validParameter;
 110
 111                         //check to make sure all parameters are valid for command
 112                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 113                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 114                         }
 115
 116                         //initialize outputTypes
 117                         vector<string> tempOutNames;
 118                         outputTypes["rarefaction"] = tempOutNames;
 119                         outputTypes["r_chao"] = tempOutNames;
 120                         outputTypes["r_ace"] = tempOutNames;
 121                         outputTypes["r_jack"] = tempOutNames;
 122                         outputTypes["r_shannon"] = tempOutNames;
 123                         outputTypes["r_shannoneven"] = tempOutNames;
 124                         outputTypes["r_heip"] = tempOutNames;
 125                         outputTypes["r_smithwilson"] = tempOutNames;
 126                         outputTypes["r_npshannon"] = tempOutNames;
 127                         outputTypes["r_simpson"] = tempOutNames;
 128                         outputTypes["r_simpsoneven"] = tempOutNames;
 129                         outputTypes["r_invsimpson"] = tempOutNames;
 130                         outputTypes["r_bootstrap"] = tempOutNames;
 131                         outputTypes["r_coverage"] = tempOutNames;
 132                         outputTypes["r_nseqs"] = tempOutNames;
 133
 134                         //if the user changes the output directory command factory will send this info to us in the output parameter
 135                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 136                                 outputDir = "";
 137                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 138                         }
 139
 140                         //make sure the user has already run the read.otu command
 141                         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; }
 142
 143                         //check for optional parameter and set defaults
 144                         // ...at some point should added some additional type checking...
 145                         label = validParameter.validFile(parameters, "label", false);
 146                         if (label == "not found") { label = ""; }
 147                         else {
 148                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 149                                 else { allLines = 1;  }
 150                         }
 151
 152                         //if the user has not specified any labels use the ones from read.otu
 153                         if(label == "") {
 154                                 allLines = globaldata->allLines;
 155                                 labels = globaldata->labels;
 156                         }
 157
 158                         calc = validParameter.validFile(parameters, "calc", false);
 159                         if (calc == "not found") { calc = "sobs";  }
 160                         else {
 161                                  if (calc == "default")  {  calc = "sobs";  }
 162                         }
 163                         m->splitAtDash(calc, Estimators);
 164
 165                         string temp;
 166                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 167                         convert(temp, freq);
 168
 169                         temp = validParameter.validFile(parameters, "abund", false);                    if (temp == "not found") { temp = "10"; }
 170                         convert(temp, abund);
 171
 172                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
 173                         convert(temp, nIters);
 174
 175                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 176                         convert(temp, processors);
 177                 }
 178
 179         }
 180         catch(exception& e) {
 181                 m->errorOut(e, "RareFactCommand", "RareFactCommand");
 182                 exit(1);
 183         }
 184 }
 185 //**********************************************************************************************************************
 186
 187 void RareFactCommand::help(){
 188         try {
 189                 m->mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
 190                 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");
 191                 m->mothurOut("The rarefaction.single command parameters are label, iters, freq, calc, processors and abund.  No parameters are required. \n");
 192                 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");
 193                 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
 194                 m->mothurOut("The rarefaction.single command should be in the following format: \n");
 195                 m->mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
 196                 m->mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
 197                 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");
 198                 validCalculator->printCalc("rarefaction", cout);
 199                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 200                 m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
 201         }
 202         catch(exception& e) {
 203                 m->errorOut(e, "RareFactCommand", "help");
 204                 exit(1);
 205         }
 206 }
 207
 208 //**********************************************************************************************************************
 209
 210 RareFactCommand::~RareFactCommand(){}
 211
 212 //**********************************************************************************************************************
 213
 214 int RareFactCommand::execute(){
 215         try {
 216
 217                 if (abort == true) { return 0; }
 218
 219                 string hadShared = "";
 220                 if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
 221                 else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
 222
 223                 if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 224
 225                 for (int p = 0; p < inputFileNames.size(); p++) {
 226
 227                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
 228                         globaldata->inputFileName = inputFileNames[p];
 229
 230                         if (m->control_pressed) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
 231
 232                         if (inputFileNames.size() > 1) {
 233                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 234                         }
 235                         int i;
 236                         validCalculator = new ValidCalculators();
 237
 238
 239                         for (i=0; i<Estimators.size(); i++) {
 240                                 if (validCalculator->isValidCalculator("rarefaction", Estimators[i]) == true) {
 241                                         if (Estimators[i] == "sobs") {
 242                                                 rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
 243                                                 outputNames.push_back(fileNameRoot+"rarefaction"); outputTypes["rarefaction"].push_back(fileNameRoot+"rarefaction");
 244                                         }else if (Estimators[i] == "chao") {
 245                                                 rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
 246                                                 outputNames.push_back(fileNameRoot+"r_chao"); outputTypes["r_chao"].push_back(fileNameRoot+"r_chao");
 247                                         }else if (Estimators[i] == "ace") {
 248                                                 if(abund < 5)
 249                                                         abund = 10;
 250                                                 rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
 251                                                 outputNames.push_back(fileNameRoot+"r_ace"); outputTypes["r_ace"].push_back(fileNameRoot+"r_ace");
 252                                         }else if (Estimators[i] == "jack") {
 253                                                 rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
 254                                                 outputNames.push_back(fileNameRoot+"r_jack"); outputTypes["r_jack"].push_back(fileNameRoot+"r_jack");
 255                                         }else if (Estimators[i] == "shannon") {
 256                                                 rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
 257                                                 outputNames.push_back(fileNameRoot+"r_shannon"); outputTypes["r_shannon"].push_back(fileNameRoot+"r_shannon");
 258                                         }else if (Estimators[i] == "shannoneven") {
 259                                                 rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
 260                                                 outputNames.push_back(fileNameRoot+"r_shannoneven"); outputTypes["r_shannoneven"].push_back(fileNameRoot+"r_shannoneven");
 261                                         }else if (Estimators[i] == "heip") {
 262                                                 rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
 263                                                 outputNames.push_back(fileNameRoot+"r_heip"); outputTypes["r_heip"].push_back(fileNameRoot+"r_heip");
 264                                         }else if (Estimators[i] == "smithwilson") {
 265                                                 rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
 266                                                 outputNames.push_back(fileNameRoot+"r_smithwilson"); outputTypes["r_smithwilson"].push_back(fileNameRoot+"r_smithwilson");
 267                                         }else if (Estimators[i] == "npshannon") {
 268                                                 rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
 269                                                 outputNames.push_back(fileNameRoot+"r_npshannon"); outputTypes["r_npshannon"].push_back(fileNameRoot+"r_npshannon");
 270                                         }else if (Estimators[i] == "simpson") {
 271                                                 rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
 272                                                 outputNames.push_back(fileNameRoot+"r_simpson"); outputTypes["r_simpson"].push_back(fileNameRoot+"r_simpson");
 273                                         }else if (Estimators[i] == "simpsoneven") {
 274                                                 rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
 275                                                 outputNames.push_back(fileNameRoot+"r_simpsoneven"); outputTypes["r_simpsoneven"].push_back(fileNameRoot+"r_simpsoneven");
 276                                         }else if (Estimators[i] == "invsimpson") {
 277                                                 rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
 278                                                 outputNames.push_back(fileNameRoot+"r_invsimpson"); outputTypes["r_invsimpson"].push_back(fileNameRoot+"r_invsimpson");
 279                                         }else if (Estimators[i] == "bootstrap") {
 280                                                 rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
 281                                                 outputNames.push_back(fileNameRoot+"r_bootstrap"); outputTypes["r_bootstrap"].push_back(fileNameRoot+"r_bootstrap");
 282                                         }else if (Estimators[i] == "coverage") {
 283                                                 rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
 284                                                 outputNames.push_back(fileNameRoot+"r_coverage"); outputTypes["r_coverage"].push_back(fileNameRoot+"r_coverage");
 285                                         }else if (Estimators[i] == "nseqs") {
 286                                                 rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
 287                                                 outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs");
 288                                         }
 289                                 }
 290                         }
 291
 292
 293                         //if the users entered no valid calculators don't execute command
 294                         if (rDisplays.size() == 0) { for(int i=0;i<rDisplays.size();i++){       delete rDisplays[i];    } delete validCalculator; return 0; }
 295
 296                         read = new ReadOTUFile(globaldata->inputFileName);
 297                         read->read(&*globaldata);
 298
 299                         order = globaldata->gorder;
 300                         string lastLabel = order->getLabel();
 301                         input = globaldata->ginput;
 302
 303                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 304                         set<string> processedLabels;
 305                         set<string> userLabels = labels;
 306
 307                         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; }
 308
 309                         //as long as you are not at the end of the file or done wih the lines you want
 310                         while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 311
 312                                 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; }
 313
 314
 315                                 if(allLines == 1 || labels.count(order->getLabel()) == 1){
 316
 317                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 318                                         rCurve = new Rarefact(order, rDisplays, processors);
 319                                         rCurve->getCurve(freq, nIters);
 320                                         delete rCurve;
 321
 322                                         processedLabels.insert(order->getLabel());
 323                                         userLabels.erase(order->getLabel());
 324                                 }
 325
 326                                 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 327                                         string saveLabel = order->getLabel();
 328
 329                                         delete order;
 330                                         order = (input->getOrderVector(lastLabel));
 331
 332                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 333                                         rCurve = new Rarefact(order, rDisplays, processors);
 334                                         rCurve->getCurve(freq, nIters);
 335                                         delete rCurve;
 336
 337                                         processedLabels.insert(order->getLabel());
 338                                         userLabels.erase(order->getLabel());
 339
 340                                         //restore real lastlabel to save below
 341                                         order->setLabel(saveLabel);
 342                                 }
 343
 344                                 lastLabel = order->getLabel();
 345
 346                                 delete order;
 347                                 order = (input->getOrderVector());
 348                         }
 349
 350                         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; }
 351
 352                         //output error messages about any remaining user labels
 353                         set<string>::iterator it;
 354                         bool needToRun = false;
 355                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 356                                 m->mothurOut("Your file does not include the label " + *it);
 357                                 if (processedLabels.count(lastLabel) != 1) {
 358                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 359                                         needToRun = true;
 360                                 }else {
 361                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 362                                 }
 363                         }
 364
 365                         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; }
 366
 367                         //run last label if you need to
 368                         if (needToRun == true)  {
 369                                 if (order != NULL) {    delete order;   }
 370                                 order = (input->getOrderVector(lastLabel));
 371
 372                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 373                                 rCurve = new Rarefact(order, rDisplays, processors);
 374                                 rCurve->getCurve(freq, nIters);
 375                                 delete rCurve;
 376
 377                                 delete order;
 378                         }
 379
 380
 381                         for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 382                         rDisplays.clear();
 383                         globaldata->gorder = NULL;
 384                         delete input;  globaldata->ginput = NULL;
 385                         delete read;
 386                         delete validCalculator;
 387
 388                 }
 389
 390                 if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  }
 391
 392                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } return 0; }
 393
 394                 m->mothurOutEndLine();
 395                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 396                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 397                 m->mothurOutEndLine();
 398
 399                 return 0;
 400         }
 401         catch(exception& e) {
 402                 m->errorOut(e, "RareFactCommand", "execute");
 403                 exit(1);
 404         }
 405 }
 406 //**********************************************************************************************************************
 407 vector<string> RareFactCommand::parseSharedFile(string filename) {
 408         try {
 409                 vector<string> filenames;
 410
 411                 map<string, ofstream*> filehandles;
 412                 map<string, ofstream*>::iterator it3;
 413
 414
 415                 //read first line
 416                 read = new ReadOTUFile(filename);
 417                 read->read(&*globaldata);
 418
 419                 input = globaldata->ginput;
 420                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 421
 422                 string sharedFileRoot = m->getRootName(filename);
 423
 424                 //clears file before we start to write to it below
 425                 for (int i=0; i<lookup.size(); i++) {
 426                         remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
 427                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 428                 }
 429
 430                 ofstream* temp;
 431                 for (int i=0; i<lookup.size(); i++) {
 432                         temp = new ofstream;
 433                         filehandles[lookup[i]->getGroup()] = temp;
 434                         groups.push_back(lookup[i]->getGroup());
 435                 }
 436
 437                 while(lookup[0] != NULL) {
 438
 439                         for (int i = 0; i < lookup.size(); i++) {
 440                                 RAbundVector rav = lookup[i]->getRAbundVector();
 441                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 442                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 443                                 (*(filehandles[lookup[i]->getGroup()])).close();
 444                         }
 445
 446                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 447                         lookup = input->getSharedRAbundVectors();
 448                 }
 449
 450                 //free memory
 451                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 452                         delete it3->second;
 453                 }
 454                 delete read;
 455                 delete input;
 456                 globaldata->ginput = NULL;
 457
 458                 return filenames;
 459         }
 460         catch(exception& e) {
 461                 m->errorOut(e, "RareFactCommand", "parseSharedFile");
 462                 exit(1);
 463         }
 464 }
 465 //**********************************************************************************************************************
 466
 467
 468