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                 abort = true; calledHelp = true;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["csv"] = tempOutNames;
  32                 outputTypes["summary"] = tempOutNames;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 vector<string> CatchAllCommand::getRequiredParameters(){
  41         try {
  42                 string AlignArray[] =  {"sabund","shared","or"};
  43                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  44                 return myArray;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 vector<string> CatchAllCommand::getRequiredFiles(){
  53         try {
  54                 vector<string> myArray;
  55                 return myArray;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
  59                 exit(1);
  60         }
  61 }
  62 /**************************************************************************************/
  63 CatchAllCommand::CatchAllCommand(string option)  {
  64         try {
  65                 globaldata = GlobalData::getInstance();
  66                 abort = false; calledHelp = false;
  67                 allLines = 1;
  68
  69                 //allow user to run help
  70                 if(option == "help") { help(); abort = true; calledHelp = true; }
  71
  72                 else {
  73                         //valid paramters for this command
  74                         string Array[] =  {"shared","sabund","label","inputdir","outputdir"};
  75                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  76
  77                         OptionParser parser(option);
  78                         map<string,string> parameters = parser.getParameters();
  79
  80                         ValidParameters validParameter;
  81                         map<string, string>::iterator it;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  86                         }
  87
  88                         //initialize outputTypes
  89                         vector<string> tempOutNames;
  90                         outputTypes["csv"] = tempOutNames;
  91                         outputTypes["summary"] = tempOutNames;
  92
  93                         //if the user changes the input directory command factory will send this info to us in the output parameter
  94                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  95                         if (inputDir == "not found"){   inputDir = "";          }
  96                         else {
  97                                 string path;
  98                                 it = parameters.find("sabund");
  99                                 //user has given a template file
 100                                 if(it != parameters.end()){
 101                                         path = m->hasPath(it->second);
 102                                         //if the user has not given a path then, add inputdir. else leave path alone.
 103                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 104                                 }
 105
 106                                 it = parameters.find("shared");
 107                                 //user has given a template file
 108                                 if(it != parameters.end()){
 109                                         path = m->hasPath(it->second);
 110                                         //if the user has not given a path then, add inputdir. else leave path alone.
 111                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 112                                 }
 113                         }
 114
 115                         //check for required parameters
 116                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 117                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 118                         else if (sabundfile == "not found") { sabundfile = "";  }
 119                         else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 120
 121                         sharedfile = validParameter.validFile(parameters, "shared", true);
 122                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 123                         else if (sharedfile == "not found") { sharedfile = "";   }
 124
 125                         //check for shared file loaded during read.otu
 126                         if (sharedfile == "") {
 127                                 if (globaldata->getSharedFile() != "") { sharedfile = globaldata->getSharedFile(); }
 128                         }
 129
 130                         string label = validParameter.validFile(parameters, "label", false);
 131                         if (label == "not found") { label = ""; }
 132                         else {
 133                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 134                                 else { allLines = 1;  }
 135                         }
 136
 137                         if ((sharedfile == "") && (sabundfile == "")) { m->mothurOut("You must provide a sabund or shared file for the catchall command."); m->mothurOutEndLine(); abort=true; }
 138
 139                         //if the user changes the output directory command factory will send this info to us in the output parameter
 140                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 141                         if (outputDir == "not found"){
 142                                 if (sabundfile != "") {  outputDir = m->hasPath(sabundfile); }
 143                                 else { outputDir = m->hasPath(sharedfile); }
 144                         }
 145                 }
 146
 147         }
 148         catch(exception& e) {
 149                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
 150                 exit(1);
 151         }
 152 }
 153 //**********************************************************************************************************************
 154
 155 void CatchAllCommand::help(){
 156         try {
 157                 m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
 158                 m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
 159                 m->mothurOut("The catchall executable must be in the same folder as your mothur executable. \n");
 160                 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");
 161                 m->mothurOut("The catchall command parameters are shared, sabund and label.  shared or sabund is required. \n");
 162                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 163                 m->mothurOut("The catchall command should be in the following format: \n");
 164                 m->mothurOut("catchall(sabund=yourSabundFile) \n");
 165                 m->mothurOut("Example: catchall(sabund=abrecovery.fn.sabund) \n");
 166         }
 167         catch(exception& e) {
 168                 m->errorOut(e, "CatchAllCommand", "help");
 169                 exit(1);
 170         }
 171 }
 172
 173 /**************************************************************************************/
 174 int CatchAllCommand::execute() {
 175         try {
 176
 177                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 178
 179                 //prepare full output directory
 180                 outputDir = m->getFullPathName(outputDir);
 181
 182                 //get location of catchall
 183                 GlobalData* globaldata = GlobalData::getInstance();
 184                 path = globaldata->argv;
 185                 path = path.substr(0, (path.find_last_of('m')));
 186                 path = m->getFullPathName(path);
 187
 188                 string catchAllCommandExe = "";
 189                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 190                         catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
 191                 #else
 192                         catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
 193                 #endif
 194
 195                 vector<string> inputFileNames;
 196                 if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile);  globaldata->setFormat("sabund");  }
 197                 else {  inputFileNames.push_back(sabundfile);  }
 198
 199                 for (int p = 0; p < inputFileNames.size(); p++) {
 200                         if (inputFileNames.size() > 1) {
 201                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 202                         }
 203
 204                         InputData* input = new InputData(inputFileNames[p], "sabund");
 205                         SAbundVector* sabund = input->getSAbundVector();
 206                         string lastLabel = sabund->getLabel();
 207
 208                         set<string> processedLabels;
 209                         set<string> userLabels = labels;
 210
 211                         string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "catchall.summary";
 212                         summaryfilename = m->getFullPathName(summaryfilename);
 213
 214                         ofstream out;
 215                         m->openOutputFile(summaryfilename, out);
 216
 217                         out << "label\tmodel\testimate\tlci\tuci" << endl;
 218
 219                         //for each label the user selected
 220                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 221
 222
 223                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 224                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 225
 226                                                 //create catchall input file from mothur's inputfile
 227                                                 string filename = process(sabund, inputFileNames[p]);
 228                                                 string outputPath = m->getPathName(filename);
 229
 230                                                 //create system command
 231                                                 string catchAllCommand = "";
 232                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 233                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 234                                                 #else
 235                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 236                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 237                                                         //wrap entire string in ""
 238                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 239                                                 #endif
 240                                                                                 //run catchall
 241                                                 system(catchAllCommand.c_str());
 242
 243                                                 remove(filename.c_str());
 244
 245                                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 246
 247                                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 248                                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 249                                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 250                                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 251
 252                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 253
 254                                                 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; }
 255
 256                                                 processedLabels.insert(sabund->getLabel());
 257                                                 userLabels.erase(sabund->getLabel());
 258                                 }
 259
 260                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 261                                                 string saveLabel = sabund->getLabel();
 262
 263                                                 delete sabund;
 264                                                 sabund = (input->getSAbundVector(lastLabel));
 265
 266                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 267
 268
 269                                                 //create catchall input file from mothur's inputfile
 270                                                 string filename = process(sabund, inputFileNames[p]);
 271                                                 string outputPath = m->getPathName(filename);
 272
 273                                                 //create system command
 274                                                 string catchAllCommand = "";
 275                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 276                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 277                                                 #else
 278                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 279                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 280                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 281                                                 #endif
 282
 283                                                 //run catchall
 284                                                 system(catchAllCommand.c_str());
 285
 286                                                 remove(filename.c_str());
 287
 288                                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 289
 290                                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 291                                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 292                                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 293                                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 294
 295                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 296
 297                                                 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; }
 298
 299                                                 processedLabels.insert(sabund->getLabel());
 300                                                 userLabels.erase(sabund->getLabel());
 301
 302                                                 //restore real lastlabel to save below
 303                                                 sabund->setLabel(saveLabel);
 304                                 }
 305
 306
 307                                 lastLabel = sabund->getLabel();
 308
 309                                 delete sabund;
 310                                 sabund = (input->getSAbundVector());
 311                         }
 312
 313                         //output error messages about any remaining user labels
 314                         set<string>::iterator it;
 315                         bool needToRun = false;
 316                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 317                                 m->mothurOut("Your file does not include the label " + *it);
 318                                 if (processedLabels.count(lastLabel) != 1) {
 319                                         m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 320                                         needToRun = true;
 321                                 }else {
 322                                         m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 323                                 }
 324                         }
 325
 326                         //run last label if you need to
 327                         if (needToRun == true)  {
 328                                 if (sabund != NULL) {   delete sabund;  }
 329                                 sabund = (input->getSAbundVector(lastLabel));
 330
 331                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 332
 333                                 //create catchall input file from mothur's inputfile
 334                                 string filename = process(sabund, inputFileNames[p]);
 335                                 string outputPath = m->getPathName(filename);
 336
 337                                 //create system command
 338                                 string catchAllCommand = "";
 339                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 340                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 341                                 #else
 342                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 343                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 344                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 345                                 #endif
 346
 347                                 //run catchall
 348                                 system(catchAllCommand.c_str());
 349
 350                                 remove(filename.c_str());
 351
 352                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 353
 354                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 355                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 356                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 357                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 358
 359                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 360
 361                                 delete sabund;
 362                         }
 363
 364                         out.close();
 365                         delete input;
 366
 367                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
 368
 369                 }
 370
 371                 if (sharedfile == "") {
 372                         string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
 373                         summaryfilename = m->getFullPathName(summaryfilename);
 374                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 375                 }else { //combine summaries
 376                         vector<string> sumNames;
 377                         for (int i = 0; i < inputFileNames.size(); i++) {
 378                                 sumNames.push_back(m->getFullPathName(outputDir + m->getRootName(m->getSimpleName(inputFileNames[i])) + "catchall.summary"));
 379                         }
 380                         string summaryfilename = combineSummmary(sumNames);
 381                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 382                 }
 383
 384                 m->mothurOutEndLine();
 385                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 386                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 387                 m->mothurOutEndLine();
 388
 389
 390                 return 0;
 391         }
 392         catch(exception& e) {
 393                 m->errorOut(e, "CatchAllCommand", "execute");
 394                 exit(1);
 395         }
 396 }
 397 //**********************************************************************************************************************
 398 string CatchAllCommand::process(SAbundVector* sabund, string file1) {
 399         try {
 400                 string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv";
 401                 filename = m->getFullPathName(filename);
 402
 403                 ofstream out;
 404                 m->openOutputFile(filename, out);
 405
 406                 for (int i = 1; i <= sabund->getMaxRank(); i++) {
 407                         int temp = sabund->get(i);
 408
 409                         if (temp != 0) {
 410                                 out << i << "," << temp << endl;
 411                         }
 412                 }
 413                 out.close();
 414
 415                 return filename;
 416
 417         }
 418         catch(exception& e) {
 419                 m->errorOut(e, "CatchAllCommand", "process");
 420                 exit(1);
 421         }
 422 }
 423 //*********************************************************************************************************************
 424 string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
 425         try {
 426
 427                 ofstream out;
 428                 string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
 429
 430                 //open combined file
 431                 m->openOutputFile(combineFileName, out);
 432
 433                 out << "label\tgroup\tmodel\testimate\tlci\tuci" << endl;
 434
 435                 //open each groups summary file
 436                 string newLabel = "";
 437                 int numLines = 0;
 438                 map<string, vector<string> > files;
 439                 for (int i=0; i<outputNames.size(); i++) {
 440                         vector<string> thisFilesLines;
 441
 442                         ifstream temp;
 443                         m->openInputFile(outputNames[i], temp);
 444
 445                         //read through first line - labels
 446                         m->getline(temp);
 447                         m->gobble(temp);
 448
 449                         //for each label
 450                         while (!temp.eof()) {
 451
 452                                 string thisLine = "";
 453                                 string tempLabel;
 454
 455                                 for (int j = 0; j < 5; j++) {
 456                                         temp >> tempLabel;
 457
 458                                         //save for later
 459                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 460                                         else{  thisLine += tempLabel + "\t";    }
 461                                 }
 462
 463                                 thisLine += "\n";
 464
 465                                 thisFilesLines.push_back(thisLine);
 466
 467                                 m->gobble(temp);
 468                         }
 469
 470                         files[outputNames[i]] = thisFilesLines;
 471
 472                         numLines = thisFilesLines.size();
 473
 474                         temp.close();
 475                         remove(outputNames[i].c_str());
 476                 }
 477
 478                 //for each label
 479                 for (int k = 0; k < numLines; k++) {
 480
 481                         //grab summary data for each group
 482                         for (int i=0; i<outputNames.size(); i++) {
 483                                 out << files[outputNames[i]][k];
 484                         }
 485                 }
 486
 487
 488                 out.close();
 489
 490                 //return combine file name
 491                 return combineFileName;
 492
 493         }
 494         catch(exception& e) {
 495                 m->errorOut(e, "CatchAllCommand", "combineSummmary");
 496                 exit(1);
 497         }
 498 }
 499 //**********************************************************************************************************************
 500 int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out) {
 501         try {
 502
 503                 ifstream in;
 504                 int able = m->openInputFile(file1, in, "noerror");
 505
 506                 if (able == 1) {  m->mothurOut("[ERROR]: the catchall program did not run properly. Please check to make sure it is located in the same folder as your mothur executable.");m->mothurOutEndLine();  m->control_pressed = true; return 0; }
 507
 508                 if (!in.eof()) {
 509
 510                         string header = m->getline(in); m->gobble(in);
 511
 512                         int pos = header.find("Total Number of Observed Species =");
 513                         string numString = "";
 514
 515
 516                         if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); }
 517                         else {
 518                                 //pos will be the position of the T in total, so we want to count to the position of =
 519                                 pos += 34;
 520                                 char c=header[pos];
 521                                 while (c != ','){
 522                                         if (c != ' ') {
 523                                                 numString += c;
 524                                         }
 525                                         pos++;
 526                                         c=header[pos];
 527
 528                                         //sanity check
 529                                         if (pos > header.length()) { m->mothurOut("Cannot find number of OTUs in " + file1); m->mothurOutEndLine(); in.close(); return 0; }
 530                                 }
 531                         }
 532
 533                         string firstline = m->getline(in); m->gobble(in);
 534                         vector<string> values;
 535                         m->splitAtComma(firstline, values);
 536
 537                         values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 538
 539                         if (values.size() == 1) { //grab next line if firstline didn't have what you wanted
 540                                 string secondline = m->getline(in); m->gobble(in);
 541                                 values.clear();
 542                                 m->splitAtComma(secondline, values);
 543
 544                                 values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 545                         }
 546
 547                         if (values.size() == 1) { //still not what we wanted fill values with numOTUs
 548                                 values.resize(8, "");
 549                                 values[1] = "Sobs";
 550                                 values[4] = numString;
 551                                 values[6] = numString;
 552                                 values[7] = numString;
 553                         }
 554
 555                         if (values.size() < 8) { values.resize(8, ""); }
 556
 557                         out << label << '\t' << values[1] << '\t' << values[4] << '\t' << values[6] << '\t' << values[7] << endl;
 558                 }
 559
 560                 in.close();
 561
 562                 return 0;
 563
 564         }
 565         catch(exception& e) {
 566                 m->errorOut(e, "CatchAllCommand", "createSummaryFile");
 567                 exit(1);
 568         }
 569 }
 570 //**********************************************************************************************************************
 571 vector<string> CatchAllCommand::parseSharedFile(string filename) {
 572         try {
 573                 vector<string> filenames;
 574
 575                 //read first line
 576                 InputData* input = new InputData(filename, "sharedfile");
 577                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 578
 579                 string sharedFileRoot = outputDir + m->getRootName(m->getSimpleName(filename));
 580
 581                 //clears file before we start to write to it below
 582                 for (int i=0; i<lookup.size(); i++) {
 583                         remove((sharedFileRoot + lookup[i]->getGroup() + ".sabund").c_str());
 584                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
 585                         groups.push_back(lookup[i]->getGroup());
 586                 }
 587
 588                 while(lookup[0] != NULL) {
 589
 590                         for (int i = 0; i < lookup.size(); i++) {
 591                                 SAbundVector sav = lookup[i]->getSAbundVector();
 592                                 ofstream out;
 593                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".sabund", out);
 594                                 sav.print(out);
 595                                 out.close();
 596                         }
 597
 598                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 599                         lookup = input->getSharedRAbundVectors();
 600                 }
 601
 602                 delete input;
 603
 604                 return filenames;
 605         }
 606         catch(exception& e) {
 607                 m->errorOut(e, "CatchAllCommand", "parseSharedFile");
 608                 exit(1);
 609         }
 610 }
 611 /**************************************************************************************/