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                         else { m->setSabundFile(sabundfile); }
 123
 124                         sharedfile = validParameter.validFile(parameters, "shared", true);
 125                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 126                         else if (sharedfile == "not found") { sharedfile = "";   }
 127                         else { m->setSharedFile(sharedfile); }
 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 == "")) {
 137                                 //is there are current file available for either of these?
 138                                 //give priority to shared, then sabund
 139                                 //if there is a current shared file, use it
 140                                 sharedfile = m->getSharedFile();
 141                                 if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 142                                 else {
 143                                         sabundfile = m->getSabundFile();
 144                                         if (sabundfile != "") {  m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 145                                         else {
 146                                                 m->mothurOut("No valid current files. You must provide a sabund or shared file before you can use the catchall command."); m->mothurOutEndLine();
 147                                                 abort = true;
 148                                         }
 149                                 }
 150                         }
 151
 152                         //if the user changes the output directory command factory will send this info to us in the output parameter
 153                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 154                         if (outputDir == "not found"){
 155                                 if (sabundfile != "") {  outputDir = m->hasPath(sabundfile); }
 156                                 else { outputDir = m->hasPath(sharedfile); }
 157                         }
 158                 }
 159
 160         }
 161         catch(exception& e) {
 162                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
 163                 exit(1);
 164         }
 165 }
 166 /**************************************************************************************/
 167 int CatchAllCommand::execute() {
 168         try {
 169
 170                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 171
 172                 //get location of catchall
 173                 path = m->argv;
 174                 path = path.substr(0, (path.find_last_of("othur")-5));
 175                 path = m->getFullPathName(path);
 176
 177         if (m->debug) { m->mothurOut("[DEBUG]: mothur's path = " + path + "\n"); }
 178
 179                 savedOutputDir = outputDir;
 180                 string catchAllCommandExe = "";
 181         string catchAllTest = "";
 182                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 183                         catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
 184                         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.
 185             catchAllTest = path + "CatchAllcmdL.exe";
 186                 #else
 187                         catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
 188                         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.
 189             catchAllTest = path + "CatchAllcmdW.exe";
 190                 #endif
 191
 192         //test to make sure formatdb exists
 193                 ifstream in;
 194                 catchAllTest = m->getFullPathName(catchAllTest);
 195                 int ableToOpen = m->openInputFile(catchAllTest, in, "no error"); in.close();
 196                 if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + catchAllTest + " file does not exist. mothur requires the catchall executable to run the catchall command."); m->mothurOutEndLine(); m->control_pressed = true; return 0;  }
 197
 198                 //prepare full output directory
 199                 outputDir = m->getFullPathName(outputDir);
 200
 201         if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + ".\n [DEBUG]: outputDir = " + outputDir + ".\n"); }
 202
 203                 vector<string> inputFileNames;
 204                 if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile);   }
 205                 else {  inputFileNames.push_back(sabundfile);  }
 206
 207                 for (int p = 0; p < inputFileNames.size(); p++) {
 208                         if (inputFileNames.size() > 1) {
 209                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 210                         }
 211
 212                         InputData input(inputFileNames[p], "sabund");
 213                         SAbundVector* sabund = input.getSAbundVector();
 214                         string lastLabel = sabund->getLabel();
 215
 216                         set<string> processedLabels;
 217                         set<string> userLabels = labels;
 218
 219                         string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "catchall.summary";
 220                         summaryfilename = m->getFullPathName(summaryfilename);
 221
 222             if (m->debug) { m->mothurOut("[DEBUG]: Input File = " + inputFileNames[p] + ".\n [DEBUG]: inputdata address = " + toString(&input) + ".\n [DEBUG]: sabund address = " + toString(&sabund) + ".\n"); }
 223
 224                         ofstream out;
 225                         m->openOutputFile(summaryfilename, out);
 226
 227                         out << "label\tmodel\testimate\tlci\tuci" << endl;
 228
 229             if (m->debug) { string open = "no"; if (out.is_open()) { open = "yes"; } m->mothurOut("[DEBUG]: output stream is open = " + open + ".\n"); }
 230
 231                         //for each label the user selected
 232                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 233
 234
 235                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 236                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 237
 238                                                 //create catchall input file from mothur's inputfile
 239                                                 string filename = process(sabund, inputFileNames[p]);
 240                                                 string outputPath = m->getPathName(filename);
 241
 242                                                 //create system command
 243                                                 string catchAllCommand = "";
 244                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 245                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 246                                                 #else
 247                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 248                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 249                                                         //wrap entire string in ""
 250                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 251                                                 #endif
 252
 253                         if (m->debug) {  m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
 254
 255                                                 //run catchall
 256                                                 system(catchAllCommand.c_str());
 257
 258                         if (m->debug) { m->mothurOut("[DEBUG]: back from system call. Keeping file: " + filename + ".\n"); }
 259
 260                         if (!m->debug) { m->mothurRemove(filename); }
 261
 262
 263                                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 264                                                 if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 265
 266                                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 267                                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 268                                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 269                                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 270
 271                         if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
 272
 273                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 274
 275                         if (m->debug) { m->mothurOut("[DEBUG]: Done creating summary file.\n"); }
 276
 277                                                 if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);   }  delete sabund;  return 0; }
 278
 279                                                 processedLabels.insert(sabund->getLabel());
 280                                                 userLabels.erase(sabund->getLabel());
 281                                 }
 282
 283                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 284                                                 string saveLabel = sabund->getLabel();
 285
 286                                                 delete sabund;
 287                                                 sabund = (input.getSAbundVector(lastLabel));
 288
 289                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 290
 291
 292                                                 //create catchall input file from mothur's inputfile
 293                                                 string filename = process(sabund, inputFileNames[p]);
 294                                                 string outputPath = m->getPathName(filename);
 295
 296                                                 //create system command
 297                                                 string catchAllCommand = "";
 298                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 299                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 300                                                 #else
 301                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 302                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 303                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 304                                                 #endif
 305
 306                         if (m->debug) {  m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
 307
 308                                                 //run catchall
 309                                                 system(catchAllCommand.c_str());
 310
 311                         if (m->debug) { m->mothurOut("[DEBUG]: back from system call. Keeping file: " + filename + ".\n"); }
 312
 313                         if (!m->debug) { m->mothurRemove(filename); }
 314
 315
 316                                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 317                                                 if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 318
 319                                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 320                                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 321                                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 322                                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 323
 324
 325                         if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
 326
 327                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 328
 329                         if (m->debug) { m->mothurOut("[DEBUG]: Done creating summary file.\n"); }
 330
 331                                                 if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);   }   delete sabund;  return 0; }
 332
 333                                                 processedLabels.insert(sabund->getLabel());
 334                                                 userLabels.erase(sabund->getLabel());
 335
 336                                                 //restore real lastlabel to save below
 337                                                 sabund->setLabel(saveLabel);
 338                                 }
 339
 340
 341                                 lastLabel = sabund->getLabel();
 342
 343                                 delete sabund;
 344                                 sabund = (input.getSAbundVector());
 345                         }
 346
 347                         //output error messages about any remaining user labels
 348                         set<string>::iterator it;
 349                         bool needToRun = false;
 350                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 351                                 m->mothurOut("Your file does not include the label " + *it);
 352                                 if (processedLabels.count(lastLabel) != 1) {
 353                                         m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 354                                         needToRun = true;
 355                                 }else {
 356                                         m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 357                                 }
 358                         }
 359
 360                         //run last label if you need to
 361                         if (needToRun == true)  {
 362                                 if (sabund != NULL) {   delete sabund;  }
 363                                 sabund = (input.getSAbundVector(lastLabel));
 364
 365                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 366
 367                                 //create catchall input file from mothur's inputfile
 368                                 string filename = process(sabund, inputFileNames[p]);
 369                                 string outputPath = m->getPathName(filename);
 370
 371                                 //create system command
 372                                 string catchAllCommand = "";
 373                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 374                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 375                                 #else
 376                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 377                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 378                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 379                                 #endif
 380
 381                 if (m->debug) {  m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
 382
 383                                 //run catchall
 384                                 system(catchAllCommand.c_str());
 385
 386                 if (m->debug) { m->mothurOut("[DEBUG]: back from system call. Keeping file: " + filename + ".\n"); }
 387
 388                                 if (!m->debug) { m->mothurRemove(filename); }
 389
 390                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 391                                 if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 392
 393                                 outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 394                                 outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 395                                 outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 396                                 outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 397                                 if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
 398
 399                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 400
 401                 if (m->debug) { m->mothurOut("[DEBUG]: Done creating summary file.\n"); }
 402
 403                                 delete sabund;
 404                         }
 405
 406                         out.close();
 407
 408                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);        } return 0; }
 409
 410                 }
 411
 412                 if (sharedfile == "") {
 413                         string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
 414                         summaryfilename = m->getFullPathName(summaryfilename);
 415                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 416                 }else { //combine summaries
 417                         vector<string> sumNames;
 418                         for (int i = 0; i < inputFileNames.size(); i++) {
 419                                 sumNames.push_back(m->getFullPathName(outputDir + m->getRootName(m->getSimpleName(inputFileNames[i])) + "catchall.summary"));
 420                         }
 421                         string summaryfilename = combineSummmary(sumNames);
 422                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 423                 }
 424
 425                 m->mothurOutEndLine();
 426                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 427                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 428                 m->mothurOutEndLine();
 429
 430
 431                 return 0;
 432         }
 433         catch(exception& e) {
 434                 m->errorOut(e, "CatchAllCommand", "execute");
 435                 exit(1);
 436         }
 437 }
 438 //**********************************************************************************************************************
 439 string CatchAllCommand::process(SAbundVector* sabund, string file1) {
 440         try {
 441                 string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv";
 442                 filename = m->getFullPathName(filename);
 443
 444                 ofstream out;
 445                 m->openOutputFile(filename, out);
 446
 447         if (m->debug) { m->mothurOut("[DEBUG]: Creating " + filename + " file for catchall, shown below.\n\n"); }
 448
 449                 for (int i = 1; i <= sabund->getMaxRank(); i++) {
 450                         int temp = sabund->get(i);
 451
 452                         if (temp != 0) {
 453                                 out << i << "," << temp << endl;
 454                 if (m->debug) { m->mothurOut(toString(i) + "," + toString(temp) + "\n"); }
 455                         }
 456                 }
 457                 out.close();
 458
 459         if (m->debug) { m->mothurOut("[DEBUG]: Done creating " + filename + " file for catchall, shown above.\n\n"); }
 460
 461                 return filename;
 462
 463         }
 464         catch(exception& e) {
 465                 m->errorOut(e, "CatchAllCommand", "process");
 466                 exit(1);
 467         }
 468 }
 469 //*********************************************************************************************************************
 470 string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
 471         try {
 472
 473                 ofstream out;
 474                 string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
 475
 476                 //open combined file
 477                 m->openOutputFile(combineFileName, out);
 478
 479                 out << "label\tgroup\tmodel\testimate\tlci\tuci" << endl;
 480
 481                 //open each groups summary file
 482                 string newLabel = "";
 483                 int numLines = 0;
 484                 map<string, vector<string> > files;
 485                 for (int i=0; i<outputNames.size(); i++) {
 486                         vector<string> thisFilesLines;
 487
 488                         ifstream temp;
 489                         m->openInputFile(outputNames[i], temp);
 490
 491                         //read through first line - labels
 492                         m->getline(temp);
 493                         m->gobble(temp);
 494
 495                         //for each label
 496                         while (!temp.eof()) {
 497
 498                                 string thisLine = "";
 499                                 string tempLabel;
 500
 501                                 for (int j = 0; j < 5; j++) {
 502                                         temp >> tempLabel;
 503
 504                                         //save for later
 505                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 506                                         else{  thisLine += tempLabel + "\t";    }
 507                                 }
 508
 509                                 thisLine += "\n";
 510
 511                                 thisFilesLines.push_back(thisLine);
 512
 513                                 m->gobble(temp);
 514                         }
 515
 516                         files[outputNames[i]] = thisFilesLines;
 517
 518                         numLines = thisFilesLines.size();
 519
 520                         temp.close();
 521                         m->mothurRemove(outputNames[i]);
 522                 }
 523
 524                 //for each label
 525                 for (int k = 0; k < numLines; k++) {
 526
 527                         //grab summary data for each group
 528                         for (int i=0; i<outputNames.size(); i++) {
 529                                 out << files[outputNames[i]][k];
 530                         }
 531                 }
 532
 533
 534                 out.close();
 535
 536                 //return combine file name
 537                 return combineFileName;
 538
 539         }
 540         catch(exception& e) {
 541                 m->errorOut(e, "CatchAllCommand", "combineSummmary");
 542                 exit(1);
 543         }
 544 }
 545 //**********************************************************************************************************************
 546 int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out) {
 547         try {
 548
 549                 ifstream in;
 550                 int able = m->openInputFile(file1, in, "noerror");
 551
 552                 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; }
 553
 554                 if (!in.eof()) {
 555
 556                         string header = m->getline(in); m->gobble(in);
 557
 558                         int pos = header.find("Total Number of Observed Species =");
 559                         string numString = "";
 560
 561
 562                         if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); }
 563                         else {
 564                                 //pos will be the position of the T in total, so we want to count to the position of =
 565                                 pos += 34;
 566                                 char c=header[pos];
 567                                 while (c != ','){
 568                                         if (c != ' ') {
 569                                                 numString += c;
 570                                         }
 571                                         pos++;
 572                                         c=header[pos];
 573
 574                                         //sanity check
 575                                         if (pos > header.length()) { m->mothurOut("Cannot find number of OTUs in " + file1); m->mothurOutEndLine(); in.close(); return 0; }
 576                                 }
 577                         }
 578
 579                         string firstline = m->getline(in); m->gobble(in);
 580                         vector<string> values;
 581                         m->splitAtComma(firstline, values);
 582
 583                         values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 584
 585                         if (values.size() == 1) { //grab next line if firstline didn't have what you wanted
 586                                 string secondline = m->getline(in); m->gobble(in);
 587                                 values.clear();
 588                                 m->splitAtComma(secondline, values);
 589
 590                                 values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 591                         }
 592
 593                         if (values.size() == 1) { //still not what we wanted fill values with numOTUs
 594                                 values.resize(8, "");
 595                                 values[1] = "Sobs";
 596                                 values[4] = numString;
 597                                 values[6] = numString;
 598                                 values[7] = numString;
 599                         }
 600
 601                         if (values.size() < 8) { values.resize(8, ""); }
 602
 603                         out << label << '\t' << values[1] << '\t' << values[4] << '\t' << values[6] << '\t' << values[7] << endl;
 604                 }
 605
 606                 in.close();
 607
 608                 return 0;
 609
 610         }
 611         catch(exception& e) {
 612                 m->errorOut(e, "CatchAllCommand", "createSummaryFile");
 613                 exit(1);
 614         }
 615 }
 616 //**********************************************************************************************************************
 617 vector<string> CatchAllCommand::parseSharedFile(string filename) {
 618         try {
 619                 vector<string> filenames;
 620
 621                 //read first line
 622                 InputData input(filename, "sharedfile");
 623                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 624
 625                 string sharedFileRoot = outputDir + m->getRootName(m->getSimpleName(filename));
 626
 627                 //clears file before we start to write to it below
 628                 for (int i=0; i<lookup.size(); i++) {
 629                         m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
 630                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
 631                         groups.push_back(lookup[i]->getGroup());
 632                 }
 633
 634                 while(lookup[0] != NULL) {
 635
 636                         for (int i = 0; i < lookup.size(); i++) {
 637                                 SAbundVector sav = lookup[i]->getSAbundVector();
 638                                 ofstream out;
 639                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".sabund", out);
 640                                 sav.print(out);
 641                                 out.close();
 642                         }
 643
 644                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 645                         lookup = input.getSharedRAbundVectors();
 646                 }
 647
 648                 return filenames;
 649         }
 650         catch(exception& e) {
 651                 m->errorOut(e, "CatchAllCommand", "parseSharedFile");
 652                 exit(1);
 653         }
 654 }
 655 /**************************************************************************************/