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
  12 //**********************************************************************************************************************
  13 vector<string> CatchAllCommand::setParameters(){
  14         try {
  15                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  16                 //can choose shared or sabund not both, so put them in the same chooseOnlyOneGroup
  17                 CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(pshared);
  18                 CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(psabund);
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "CatchAllCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string CatchAllCommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 helpString += "The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n";
  36                 helpString += "For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n";
  37                 helpString += "The catchall executable must be in the same folder as your mothur executable. \n";
  38                 helpString += "If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n";
  39                 helpString += "The catchall command parameters are shared, sabund and label.  shared or sabund is required. \n";
  40                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  41                 helpString += "The catchall command should be in the following format: \n";
  42                 helpString += "catchall(sabund=yourSabundFile) \n";
  43                 helpString += "Example: catchall(sabund=abrecovery.fn.sabund) \n";
  44                 return helpString;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "CatchAllCommand", "getHelpString");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 CatchAllCommand::CatchAllCommand(){
  53         try {
  54                 abort = true; calledHelp = true;
  55                 setParameters();
  56                 //initialize outputTypes
  57                 vector<string> tempOutNames;
  58                 outputTypes["csv"] = tempOutNames;
  59                 outputTypes["summary"] = tempOutNames;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
  63                 exit(1);
  64         }
  65 }
  66 /**************************************************************************************/
  67 CatchAllCommand::CatchAllCommand(string option)  {
  68         try {
  69
  70                 abort = false; calledHelp = false;
  71                 allLines = 1;
  72
  73                 //allow user to run help
  74                 if(option == "help") { help(); abort = true; calledHelp = true; }
  75                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  76
  77                 else {
  78                         vector<string> myArray = setParameters();
  79
  80                         OptionParser parser(option);
  81                         map<string,string> parameters = parser.getParameters();
  82
  83                         ValidParameters validParameter;
  84                         map<string, string>::iterator it;
  85
  86                         //check to make sure all parameters are valid for command
  87                         for (it = parameters.begin(); it != parameters.end(); it++) {
  88                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  89                         }
  90
  91                         //initialize outputTypes
  92                         vector<string> tempOutNames;
  93                         outputTypes["csv"] = tempOutNames;
  94                         outputTypes["summary"] = tempOutNames;
  95
  96                         //if the user changes the input directory command factory will send this info to us in the output parameter
  97                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  98                         if (inputDir == "not found"){   inputDir = "";          }
  99                         else {
 100                                 string path;
 101                                 it = parameters.find("sabund");
 102                                 //user has given a template file
 103                                 if(it != parameters.end()){
 104                                         path = m->hasPath(it->second);
 105                                         //if the user has not given a path then, add inputdir. else leave path alone.
 106                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 107                                 }
 108
 109                                 it = parameters.find("shared");
 110                                 //user has given a template file
 111                                 if(it != parameters.end()){
 112                                         path = m->hasPath(it->second);
 113                                         //if the user has not given a path then, add inputdir. else leave path alone.
 114                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 115                                 }
 116                         }
 117
 118                         //check for required parameters
 119                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 120                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 121                         else if (sabundfile == "not found") { sabundfile = "";  }
 122
 123                         sharedfile = validParameter.validFile(parameters, "shared", true);
 124                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 125                         else if (sharedfile == "not found") { sharedfile = "";   }
 126
 127                         string label = validParameter.validFile(parameters, "label", false);
 128                         if (label == "not found") { label = ""; }
 129                         else {
 130                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 131                                 else { allLines = 1;  }
 132                         }
 133
 134                         if ((sharedfile == "") && (sabundfile == "")) {
 135                                 //is there are current file available for either of these?
 136                                 //give priority to shared, then sabund
 137                                 //if there is a current shared file, use it
 138                                 sharedfile = m->getSharedFile();
 139                                 if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 140                                 else {
 141                                         sabundfile = m->getSabundFile();
 142                                         if (sabundfile != "") {  m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 143                                         else {
 144                                                 m->mothurOut("No valid current files. You must provide a sabund or shared file before you can use the catchall command."); m->mothurOutEndLine();
 145                                                 abort = true;
 146                                         }
 147                                 }
 148                         }
 149
 150                         //if the user changes the output directory command factory will send this info to us in the output parameter
 151                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 152                         if (outputDir == "not found"){
 153                                 if (sabundfile != "") {  outputDir = m->hasPath(sabundfile); }
 154                                 else { outputDir = m->hasPath(sharedfile); }
 155                         }
 156                 }
 157
 158         }
 159         catch(exception& e) {
 160                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
 161                 exit(1);
 162         }
 163 }
 164 /**************************************************************************************/
 165 int CatchAllCommand::execute() {
 166         try {
 167
 168                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 169
 170                 //get location of catchall
 171                 path = m->argv;
 172                 path = path.substr(0, (path.find_last_of("othur")-5));
 173                 path = m->getFullPathName(path);
 174
 175                 savedOutputDir = outputDir;
 176                 string catchAllCommandExe = "";
 177                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 178                         catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
 179                         if (outputDir == "") { outputDir = "./"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
 180                 #else
 181                         catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
 182                         if (outputDir == "") { outputDir = ".\\"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
 183                 #endif
 184
 185                 //prepare full output directory
 186                 outputDir = m->getFullPathName(outputDir);
 187
 188                 vector<string> inputFileNames;
 189                 if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile);   }
 190                 else {  inputFileNames.push_back(sabundfile);  }
 191
 192                 for (int p = 0; p < inputFileNames.size(); p++) {
 193                         if (inputFileNames.size() > 1) {
 194                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 195                         }
 196
 197                         InputData* input = new InputData(inputFileNames[p], "sabund");
 198                         SAbundVector* sabund = input->getSAbundVector();
 199                         string lastLabel = sabund->getLabel();
 200
 201                         set<string> processedLabels;
 202                         set<string> userLabels = labels;
 203
 204                         string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "catchall.summary";
 205                         summaryfilename = m->getFullPathName(summaryfilename);
 206
 207                         ofstream out;
 208                         m->openOutputFile(summaryfilename, out);
 209
 210                         out << "label\tmodel\testimate\tlci\tuci" << endl;
 211
 212                         //for each label the user selected
 213                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 214
 215
 216                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 217                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 218
 219                                                 //create catchall input file from mothur's inputfile
 220                                                 string filename = process(sabund, inputFileNames[p]);
 221                                                 string outputPath = m->getPathName(filename);
 222
 223                                                 //create system command
 224                                                 string catchAllCommand = "";
 225                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 226                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 227                                                 #else
 228                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 229                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 230                                                         //wrap entire string in ""
 231                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 232                                                 #endif
 233
 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                                                 if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 241
 242                                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 243                                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 244                                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 245                                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 246
 247                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 248
 249                                                 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; }
 250
 251                                                 processedLabels.insert(sabund->getLabel());
 252                                                 userLabels.erase(sabund->getLabel());
 253                                 }
 254
 255                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 256                                                 string saveLabel = sabund->getLabel();
 257
 258                                                 delete sabund;
 259                                                 sabund = (input->getSAbundVector(lastLabel));
 260
 261                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 262
 263
 264                                                 //create catchall input file from mothur's inputfile
 265                                                 string filename = process(sabund, inputFileNames[p]);
 266                                                 string outputPath = m->getPathName(filename);
 267
 268                                                 //create system command
 269                                                 string catchAllCommand = "";
 270                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 271                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 272                                                 #else
 273                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 274                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 275                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 276                                                 #endif
 277
 278                                                 //run catchall
 279                                                 system(catchAllCommand.c_str());
 280
 281                                                 remove(filename.c_str());
 282
 283                                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 284                                                 if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 285
 286                                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 287                                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 288                                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 289                                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 290
 291                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 292
 293                                                 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; }
 294
 295                                                 processedLabels.insert(sabund->getLabel());
 296                                                 userLabels.erase(sabund->getLabel());
 297
 298                                                 //restore real lastlabel to save below
 299                                                 sabund->setLabel(saveLabel);
 300                                 }
 301
 302
 303                                 lastLabel = sabund->getLabel();
 304
 305                                 delete sabund;
 306                                 sabund = (input->getSAbundVector());
 307                         }
 308
 309                         //output error messages about any remaining user labels
 310                         set<string>::iterator it;
 311                         bool needToRun = false;
 312                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 313                                 m->mothurOut("Your file does not include the label " + *it);
 314                                 if (processedLabels.count(lastLabel) != 1) {
 315                                         m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 316                                         needToRun = true;
 317                                 }else {
 318                                         m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 319                                 }
 320                         }
 321
 322                         //run last label if you need to
 323                         if (needToRun == true)  {
 324                                 if (sabund != NULL) {   delete sabund;  }
 325                                 sabund = (input->getSAbundVector(lastLabel));
 326
 327                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 328
 329                                 //create catchall input file from mothur's inputfile
 330                                 string filename = process(sabund, inputFileNames[p]);
 331                                 string outputPath = m->getPathName(filename);
 332
 333                                 //create system command
 334                                 string catchAllCommand = "";
 335                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 336                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 337                                 #else
 338                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 339                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 340                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 341                                 #endif
 342
 343                                 //run catchall
 344                                 system(catchAllCommand.c_str());
 345
 346                                 remove(filename.c_str());
 347
 348                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 349                                 if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 350
 351                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 352                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 353                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 354                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 355
 356                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 357
 358                                 delete sabund;
 359                         }
 360
 361                         out.close();
 362                         delete input;
 363
 364                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
 365
 366                 }
 367
 368                 if (sharedfile == "") {
 369                         string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
 370                         summaryfilename = m->getFullPathName(summaryfilename);
 371                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 372                 }else { //combine summaries
 373                         vector<string> sumNames;
 374                         for (int i = 0; i < inputFileNames.size(); i++) {
 375                                 sumNames.push_back(m->getFullPathName(outputDir + m->getRootName(m->getSimpleName(inputFileNames[i])) + "catchall.summary"));
 376                         }
 377                         string summaryfilename = combineSummmary(sumNames);
 378                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 379                 }
 380
 381                 m->mothurOutEndLine();
 382                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 383                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 384                 m->mothurOutEndLine();
 385
 386
 387                 return 0;
 388         }
 389         catch(exception& e) {
 390                 m->errorOut(e, "CatchAllCommand", "execute");
 391                 exit(1);
 392         }
 393 }
 394 //**********************************************************************************************************************
 395 string CatchAllCommand::process(SAbundVector* sabund, string file1) {
 396         try {
 397                 string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv";
 398                 filename = m->getFullPathName(filename);
 399
 400                 ofstream out;
 401                 m->openOutputFile(filename, out);
 402
 403                 for (int i = 1; i <= sabund->getMaxRank(); i++) {
 404                         int temp = sabund->get(i);
 405
 406                         if (temp != 0) {
 407                                 out << i << "," << temp << endl;
 408                         }
 409                 }
 410                 out.close();
 411
 412                 return filename;
 413
 414         }
 415         catch(exception& e) {
 416                 m->errorOut(e, "CatchAllCommand", "process");
 417                 exit(1);
 418         }
 419 }
 420 //*********************************************************************************************************************
 421 string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
 422         try {
 423
 424                 ofstream out;
 425                 string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
 426
 427                 //open combined file
 428                 m->openOutputFile(combineFileName, out);
 429
 430                 out << "label\tgroup\tmodel\testimate\tlci\tuci" << endl;
 431
 432                 //open each groups summary file
 433                 string newLabel = "";
 434                 int numLines = 0;
 435                 map<string, vector<string> > files;
 436                 for (int i=0; i<outputNames.size(); i++) {
 437                         vector<string> thisFilesLines;
 438
 439                         ifstream temp;
 440                         m->openInputFile(outputNames[i], temp);
 441
 442                         //read through first line - labels
 443                         m->getline(temp);
 444                         m->gobble(temp);
 445
 446                         //for each label
 447                         while (!temp.eof()) {
 448
 449                                 string thisLine = "";
 450                                 string tempLabel;
 451
 452                                 for (int j = 0; j < 5; j++) {
 453                                         temp >> tempLabel;
 454
 455                                         //save for later
 456                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 457                                         else{  thisLine += tempLabel + "\t";    }
 458                                 }
 459
 460                                 thisLine += "\n";
 461
 462                                 thisFilesLines.push_back(thisLine);
 463
 464                                 m->gobble(temp);
 465                         }
 466
 467                         files[outputNames[i]] = thisFilesLines;
 468
 469                         numLines = thisFilesLines.size();
 470
 471                         temp.close();
 472                         remove(outputNames[i].c_str());
 473                 }
 474
 475                 //for each label
 476                 for (int k = 0; k < numLines; k++) {
 477
 478                         //grab summary data for each group
 479                         for (int i=0; i<outputNames.size(); i++) {
 480                                 out << files[outputNames[i]][k];
 481                         }
 482                 }
 483
 484
 485                 out.close();
 486
 487                 //return combine file name
 488                 return combineFileName;
 489
 490         }
 491         catch(exception& e) {
 492                 m->errorOut(e, "CatchAllCommand", "combineSummmary");
 493                 exit(1);
 494         }
 495 }
 496 //**********************************************************************************************************************
 497 int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out) {
 498         try {
 499
 500                 ifstream in;
 501                 int able = m->openInputFile(file1, in, "noerror");
 502
 503                 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; }
 504
 505                 if (!in.eof()) {
 506
 507                         string header = m->getline(in); m->gobble(in);
 508
 509                         int pos = header.find("Total Number of Observed Species =");
 510                         string numString = "";
 511
 512
 513                         if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); }
 514                         else {
 515                                 //pos will be the position of the T in total, so we want to count to the position of =
 516                                 pos += 34;
 517                                 char c=header[pos];
 518                                 while (c != ','){
 519                                         if (c != ' ') {
 520                                                 numString += c;
 521                                         }
 522                                         pos++;
 523                                         c=header[pos];
 524
 525                                         //sanity check
 526                                         if (pos > header.length()) { m->mothurOut("Cannot find number of OTUs in " + file1); m->mothurOutEndLine(); in.close(); return 0; }
 527                                 }
 528                         }
 529
 530                         string firstline = m->getline(in); m->gobble(in);
 531                         vector<string> values;
 532                         m->splitAtComma(firstline, values);
 533
 534                         values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 535
 536                         if (values.size() == 1) { //grab next line if firstline didn't have what you wanted
 537                                 string secondline = m->getline(in); m->gobble(in);
 538                                 values.clear();
 539                                 m->splitAtComma(secondline, values);
 540
 541                                 values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 542                         }
 543
 544                         if (values.size() == 1) { //still not what we wanted fill values with numOTUs
 545                                 values.resize(8, "");
 546                                 values[1] = "Sobs";
 547                                 values[4] = numString;
 548                                 values[6] = numString;
 549                                 values[7] = numString;
 550                         }
 551
 552                         if (values.size() < 8) { values.resize(8, ""); }
 553
 554                         out << label << '\t' << values[1] << '\t' << values[4] << '\t' << values[6] << '\t' << values[7] << endl;
 555                 }
 556
 557                 in.close();
 558
 559                 return 0;
 560
 561         }
 562         catch(exception& e) {
 563                 m->errorOut(e, "CatchAllCommand", "createSummaryFile");
 564                 exit(1);
 565         }
 566 }
 567 //**********************************************************************************************************************
 568 vector<string> CatchAllCommand::parseSharedFile(string filename) {
 569         try {
 570                 vector<string> filenames;
 571
 572                 //read first line
 573                 InputData* input = new InputData(filename, "sharedfile");
 574                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 575
 576                 string sharedFileRoot = outputDir + m->getRootName(m->getSimpleName(filename));
 577
 578                 //clears file before we start to write to it below
 579                 for (int i=0; i<lookup.size(); i++) {
 580                         remove((sharedFileRoot + lookup[i]->getGroup() + ".sabund").c_str());
 581                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
 582                         groups.push_back(lookup[i]->getGroup());
 583                 }
 584
 585                 while(lookup[0] != NULL) {
 586
 587                         for (int i = 0; i < lookup.size(); i++) {
 588                                 SAbundVector sav = lookup[i]->getSAbundVector();
 589                                 ofstream out;
 590                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".sabund", out);
 591                                 sav.print(out);
 592                                 out.close();
 593                         }
 594
 595                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 596                         lookup = input->getSharedRAbundVectors();
 597                 }
 598
 599                 delete input;
 600
 601                 return filenames;
 602         }
 603         catch(exception& e) {
 604                 m->errorOut(e, "CatchAllCommand", "parseSharedFile");
 605                 exit(1);
 606         }
 607 }
 608 /**************************************************************************************/