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