catchallcommand.cpp

   1 /*
   2  *  catchallcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/11/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "catchallcommand.h"
  11 #include "globaldata.hpp"
  12
  13 //**********************************************************************************************************************
  14 vector<string> CatchAllCommand::getValidParameters(){
  15         try {
  16                 string AlignArray[] =  {"sabund","shared","label","inputdir","outputdir"};
  17                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "CatchAllCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 CatchAllCommand::CatchAllCommand(){
  27         try {
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["csv"] = tempOutNames;
  31                 outputTypes["summary"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> CatchAllCommand::getRequiredParameters(){
  40         try {
  41                 string AlignArray[] =  {"sabund","shared","or"};
  42                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> CatchAllCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 /**************************************************************************************/
  62 CatchAllCommand::CatchAllCommand(string option)  {
  63         try {
  64                 globaldata = GlobalData::getInstance();
  65                 abort = false;
  66                 allLines = 1;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string Array[] =  {"shared","sabund","label","inputdir","outputdir"};
  74                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string,string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80                         map<string, string>::iterator it;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86
  87                         //initialize outputTypes
  88                         vector<string> tempOutNames;
  89                         outputTypes["csv"] = tempOutNames;
  90                         outputTypes["summary"] = tempOutNames;
  91
  92                         //if the user changes the input directory command factory will send this info to us in the output parameter
  93                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  94                         if (inputDir == "not found"){   inputDir = "";          }
  95                         else {
  96                                 string path;
  97                                 it = parameters.find("sabund");
  98                                 //user has given a template file
  99                                 if(it != parameters.end()){
 100                                         path = m->hasPath(it->second);
 101                                         //if the user has not given a path then, add inputdir. else leave path alone.
 102                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 103                                 }
 104
 105                                 it = parameters.find("shared");
 106                                 //user has given a template file
 107                                 if(it != parameters.end()){
 108                                         path = m->hasPath(it->second);
 109                                         //if the user has not given a path then, add inputdir. else leave path alone.
 110                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 111                                 }
 112                         }
 113
 114                         //check for required parameters
 115                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 116                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 117                         else if (sabundfile == "not found") { sabundfile = "";  }
 118                         else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 119
 120                         sharedfile = validParameter.validFile(parameters, "shared", true);
 121                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 122                         else if (sharedfile == "not found") { sharedfile = "";   }
 123
 124                         string label = validParameter.validFile(parameters, "label", false);
 125                         if (label == "not found") { label = ""; }
 126                         else {
 127                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 128                                 else { allLines = 1;  }
 129                         }
 130
 131                         if ((sharedfile == "") && (sabundfile == "")) { m->mothurOut("You must provide a sabund or shared file for the catchall command."); m->mothurOutEndLine(); abort=true; }
 132
 133                         //if the user changes the output directory command factory will send this info to us in the output parameter
 134                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 135                         if (outputDir == "not found"){
 136                                 if (sabundfile != "") {  outputDir = m->hasPath(sabundfile); }
 137                                 else { outputDir = m->hasPath(sharedfile); }
 138                         }
 139                 }
 140
 141         }
 142         catch(exception& e) {
 143                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
 144                 exit(1);
 145         }
 146 }
 147 //**********************************************************************************************************************
 148
 149 void CatchAllCommand::help(){
 150         try {
 151                 m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
 152                 m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
 153                 m->mothurOut("The catchall executable must be in the same folder as your mothur executable. \n");
 154                 m->mothurOut("If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n");
 155                 m->mothurOut("The catchall command parameters are shared, sabund and label.  shared or sabund is required. \n");
 156                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 157                 m->mothurOut("The catchall command should be in the following format: \n");
 158                 m->mothurOut("catchall(sabund=yourSabundFile) \n");
 159                 m->mothurOut("Example: catchall(sabund=abrecovery.fn.sabund) \n");
 160         }
 161         catch(exception& e) {
 162                 m->errorOut(e, "CatchAllCommand", "help");
 163                 exit(1);
 164         }
 165 }
 166
 167 /**************************************************************************************/
 168 int CatchAllCommand::execute() {
 169         try {
 170
 171                 if (abort == true) { return 0; }
 172
 173                 //prepare full output directory
 174                 outputDir = m->getFullPathName(outputDir);
 175
 176                 //get location of catchall
 177                 GlobalData* globaldata = GlobalData::getInstance();
 178                 path = globaldata->argv;
 179                 path = path.substr(0, (path.find_last_of('m')));
 180                 path = m->getFullPathName(path);
 181
 182                 string catchAllCommandExe = "";
 183                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 184                         catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
 185                 #else
 186                         catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
 187                 #endif
 188
 189                 vector<string> inputFileNames;
 190                 if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile);  globaldata->setFormat("sabund");  }
 191                 else {  inputFileNames.push_back(sabundfile);  }
 192
 193                 for (int p = 0; p < inputFileNames.size(); p++) {
 194                         if (inputFileNames.size() > 1) {
 195                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 196                         }
 197
 198                         InputData* input = new InputData(inputFileNames[p], "sabund");
 199                         SAbundVector* sabund = input->getSAbundVector();
 200                         string lastLabel = sabund->getLabel();
 201
 202                         set<string> processedLabels;
 203                         set<string> userLabels = labels;
 204
 205                         string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "catchall.summary";
 206                         summaryfilename = m->getFullPathName(summaryfilename);
 207
 208                         ofstream out;
 209                         m->openOutputFile(summaryfilename, out);
 210
 211                         out << "label\tmodel\testimate\tlci\tuci" << endl;
 212
 213                         //for each label the user selected
 214                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 215
 216
 217                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 218                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 219
 220                                                 //create catchall input file from mothur's inputfile
 221                                                 string filename = process(sabund, inputFileNames[p]);
 222                                                 string outputPath = m->getPathName(filename);
 223
 224                                                 //create system command
 225                                                 string catchAllCommand = "";
 226                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 227                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 228                                                 #else
 229                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 230                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 231                                                         //wrap entire string in ""
 232                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 233                                                 #endif
 234                                                                                 //run catchall
 235                                                 system(catchAllCommand.c_str());
 236
 237                                                 remove(filename.c_str());
 238
 239                                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 240
 241                                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 242                                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 243                                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 244                                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 245
 246                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 247
 248                                                 if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str());    }  delete input;  delete sabund;  return 0; }
 249
 250                                                 processedLabels.insert(sabund->getLabel());
 251                                                 userLabels.erase(sabund->getLabel());
 252                                 }
 253
 254                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 255                                                 string saveLabel = sabund->getLabel();
 256
 257                                                 delete sabund;
 258                                                 sabund = (input->getSAbundVector(lastLabel));
 259
 260                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 261
 262
 263                                                 //create catchall input file from mothur's inputfile
 264                                                 string filename = process(sabund, inputFileNames[p]);
 265                                                 string outputPath = m->getPathName(filename);
 266
 267                                                 //create system command
 268                                                 string catchAllCommand = "";
 269                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 270                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 271                                                 #else
 272                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 273                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 274                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 275                                                 #endif
 276
 277                                                 //run catchall
 278                                                 system(catchAllCommand.c_str());
 279
 280                                                 remove(filename.c_str());
 281
 282                                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 283
 284                                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 285                                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 286                                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 287                                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 288
 289                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 290
 291                                                 if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str());    }  delete input;  delete sabund;  return 0; }
 292
 293                                                 processedLabels.insert(sabund->getLabel());
 294                                                 userLabels.erase(sabund->getLabel());
 295
 296                                                 //restore real lastlabel to save below
 297                                                 sabund->setLabel(saveLabel);
 298                                 }
 299
 300
 301                                 lastLabel = sabund->getLabel();
 302
 303                                 delete sabund;
 304                                 sabund = (input->getSAbundVector());
 305                         }
 306
 307                         //output error messages about any remaining user labels
 308                         set<string>::iterator it;
 309                         bool needToRun = false;
 310                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 311                                 m->mothurOut("Your file does not include the label " + *it);
 312                                 if (processedLabels.count(lastLabel) != 1) {
 313                                         m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 314                                         needToRun = true;
 315                                 }else {
 316                                         m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 317                                 }
 318                         }
 319
 320                         //run last label if you need to
 321                         if (needToRun == true)  {
 322                                 if (sabund != NULL) {   delete sabund;  }
 323                                 sabund = (input->getSAbundVector(lastLabel));
 324
 325                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 326
 327                                 //create catchall input file from mothur's inputfile
 328                                 string filename = process(sabund, inputFileNames[p]);
 329                                 string outputPath = m->getPathName(filename);
 330
 331                                 //create system command
 332                                 string catchAllCommand = "";
 333                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 334                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 335                                 #else
 336                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 337                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 338                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 339                                 #endif
 340
 341                                 //run catchall
 342                                 system(catchAllCommand.c_str());
 343
 344                                 remove(filename.c_str());
 345
 346                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 347
 348                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 349                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 350                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 351                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 352
 353                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 354
 355                                 delete sabund;
 356                         }
 357
 358                         out.close();
 359                         delete input;
 360
 361                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
 362
 363                 }
 364
 365                 if (sharedfile == "") {
 366                         string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
 367                         summaryfilename = m->getFullPathName(summaryfilename);
 368                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 369                 }else { //combine summaries
 370                         vector<string> sumNames;
 371                         for (int i = 0; i < inputFileNames.size(); i++) {
 372                                 sumNames.push_back(m->getFullPathName(outputDir + m->getRootName(m->getSimpleName(inputFileNames[i])) + "catchall.summary"));
 373                         }
 374                         string summaryfilename = combineSummmary(sumNames);
 375                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 376                 }
 377
 378                 m->mothurOutEndLine();
 379                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 380                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 381                 m->mothurOutEndLine();
 382
 383
 384                 return 0;
 385         }
 386         catch(exception& e) {
 387                 m->errorOut(e, "CatchAllCommand", "execute");
 388                 exit(1);
 389         }
 390 }
 391 //**********************************************************************************************************************
 392 string CatchAllCommand::process(SAbundVector* sabund, string file1) {
 393         try {
 394                 string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv";
 395                 filename = m->getFullPathName(filename);
 396
 397                 ofstream out;
 398                 m->openOutputFile(filename, out);
 399
 400                 for (int i = 1; i <= sabund->getMaxRank(); i++) {
 401                         int temp = sabund->get(i);
 402
 403                         if (temp != 0) {
 404                                 out << i << "," << temp << endl;
 405                         }
 406                 }
 407                 out.close();
 408
 409                 return filename;
 410
 411         }
 412         catch(exception& e) {
 413                 m->errorOut(e, "CatchAllCommand", "process");
 414                 exit(1);
 415         }
 416 }
 417 //*********************************************************************************************************************
 418 string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
 419         try {
 420
 421                 ofstream out;
 422                 string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
 423
 424                 //open combined file
 425                 m->openOutputFile(combineFileName, out);
 426
 427                 out << "label\tgroup\tmodel\testimate\tlci\tuci" << endl;
 428
 429                 //open each groups summary file
 430                 string newLabel = "";
 431                 int numLines = 0;
 432                 map<string, vector<string> > files;
 433                 for (int i=0; i<outputNames.size(); i++) {
 434                         vector<string> thisFilesLines;
 435
 436                         ifstream temp;
 437                         m->openInputFile(outputNames[i], temp);
 438
 439                         //read through first line - labels
 440                         m->getline(temp);
 441                         m->gobble(temp);
 442
 443                         //for each label
 444                         while (!temp.eof()) {
 445
 446                                 string thisLine = "";
 447                                 string tempLabel;
 448
 449                                 for (int j = 0; j < 5; j++) {
 450                                         temp >> tempLabel;
 451
 452                                         //save for later
 453                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 454                                         else{  thisLine += tempLabel + "\t";    }
 455                                 }
 456
 457                                 thisLine += "\n";
 458
 459                                 thisFilesLines.push_back(thisLine);
 460
 461                                 m->gobble(temp);
 462                         }
 463
 464                         files[outputNames[i]] = thisFilesLines;
 465
 466                         numLines = thisFilesLines.size();
 467
 468                         temp.close();
 469                         remove(outputNames[i].c_str());
 470                 }
 471
 472                 //for each label
 473                 for (int k = 0; k < numLines; k++) {
 474
 475                         //grab summary data for each group
 476                         for (int i=0; i<outputNames.size(); i++) {
 477                                 out << files[outputNames[i]][k];
 478                         }
 479                 }
 480
 481
 482                 out.close();
 483
 484                 //return combine file name
 485                 return combineFileName;
 486
 487         }
 488         catch(exception& e) {
 489                 m->errorOut(e, "CatchAllCommand", "combineSummmary");
 490                 exit(1);
 491         }
 492 }
 493 //**********************************************************************************************************************
 494 int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out) {
 495         try {
 496
 497                 ifstream in;
 498                 m->openInputFile(file1, in);
 499
 500                 if (!in.eof()) {
 501
 502                         string header = m->getline(in); m->gobble(in);
 503
 504                         int pos = header.find("Total Number of Observed Species =");
 505                         string numString = "";
 506
 507
 508                         if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); }
 509                         else {
 510                                 //pos will be the position of the T in total, so we want to count to the position of =
 511                                 pos += 34;
 512                                 char c=header[pos];
 513                                 while (c != ','){
 514                                         if (c != ' ') {
 515                                                 numString += c;
 516                                         }
 517                                         pos++;
 518                                         c=header[pos];
 519
 520                                         //sanity check
 521                                         if (pos > header.length()) { m->mothurOut("Cannot find number of OTUs in " + file1); m->mothurOutEndLine(); in.close(); return 0; }
 522                                 }
 523                         }
 524
 525                         string firstline = m->getline(in); m->gobble(in);
 526                         vector<string> values;
 527                         m->splitAtComma(firstline, values);
 528
 529                         values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 530
 531                         if (values.size() == 1) { //grab next line if firstline didn't have what you wanted
 532                                 string secondline = m->getline(in); m->gobble(in);
 533                                 values.clear();
 534                                 m->splitAtComma(secondline, values);
 535
 536                                 values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 537                         }
 538
 539                         if (values.size() == 1) { //still not what we wanted fill values with numOTUs
 540                                 values.resize(8, "");
 541                                 values[1] = "Sobs";
 542                                 values[4] = numString;
 543                                 values[6] = numString;
 544                                 values[7] = numString;
 545                         }
 546
 547                         if (values.size() < 8) { values.resize(8, ""); }
 548
 549                         out << label << '\t' << values[1] << '\t' << values[4] << '\t' << values[6] << '\t' << values[7] << endl;
 550                 }
 551
 552                 in.close();
 553
 554                 return 0;
 555
 556         }
 557         catch(exception& e) {
 558                 m->errorOut(e, "CatchAllCommand", "createSummaryFile");
 559                 exit(1);
 560         }
 561 }
 562 //**********************************************************************************************************************
 563 vector<string> CatchAllCommand::parseSharedFile(string filename) {
 564         try {
 565                 vector<string> filenames;
 566
 567                 //read first line
 568                 InputData* input = new InputData(filename, "sharedfile");
 569                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 570
 571                 string sharedFileRoot = outputDir + m->getRootName(m->getSimpleName(filename));
 572
 573                 //clears file before we start to write to it below
 574                 for (int i=0; i<lookup.size(); i++) {
 575                         remove((sharedFileRoot + lookup[i]->getGroup() + ".sabund").c_str());
 576                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
 577                         groups.push_back(lookup[i]->getGroup());
 578                 }
 579
 580                 while(lookup[0] != NULL) {
 581
 582                         for (int i = 0; i < lookup.size(); i++) {
 583                                 SAbundVector sav = lookup[i]->getSAbundVector();
 584                                 ofstream out;
 585                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".sabund", out);
 586                                 sav.print(out);
 587                                 out.close();
 588                         }
 589
 590                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 591                         lookup = input->getSharedRAbundVectors();
 592                 }
 593
 594                 delete input;
 595
 596                 return filenames;
 597         }
 598         catch(exception& e) {
 599                 m->errorOut(e, "CatchAllCommand", "parseSharedFile");
 600                 exit(1);
 601         }
 602 }
 603 /**************************************************************************************/