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 string CatchAllCommand::getOutputFileNameTag(string type, string inputName=""){
  53         try {
  54         string outputFileName = "";
  55                 map<string, vector<string> >::iterator it;
  56
  57         //is this a type this command creates
  58         it = outputTypes.find(type);
  59         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  60         else {
  61             if (type == "csv") {  outputFileName =  "csv"; }
  62             else if (type == "summary") {  outputFileName =  "catchall.summary"; }
  63             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  64         }
  65         return outputFileName;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "CatchAllCommand", "getOutputFileNameTag");
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73 CatchAllCommand::CatchAllCommand(){
  74         try {
  75                 abort = true; calledHelp = true;
  76                 setParameters();
  77                 //initialize outputTypes
  78                 vector<string> tempOutNames;
  79                 outputTypes["csv"] = tempOutNames;
  80                 outputTypes["summary"] = tempOutNames;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
  84                 exit(1);
  85         }
  86 }
  87 /**************************************************************************************/
  88 CatchAllCommand::CatchAllCommand(string option)  {
  89         try {
  90
  91                 abort = false; calledHelp = false;
  92                 allLines = 1;
  93
  94                 //allow user to run help
  95                 if(option == "help") { help(); abort = true; calledHelp = true; }
  96                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  97
  98                 else {
  99                         vector<string> myArray = setParameters();
 100
 101                         OptionParser parser(option);
 102                         map<string,string> parameters = parser.getParameters();
 103
 104                         ValidParameters validParameter;
 105                         map<string, string>::iterator it;
 106
 107                         //check to make sure all parameters are valid for command
 108                         for (it = parameters.begin(); it != parameters.end(); it++) {
 109                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 110                         }
 111
 112                         //initialize outputTypes
 113                         vector<string> tempOutNames;
 114                         outputTypes["csv"] = tempOutNames;
 115                         outputTypes["summary"] = tempOutNames;
 116
 117                         //if the user changes the input directory command factory will send this info to us in the output parameter
 118                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 119                         if (inputDir == "not found"){   inputDir = "";          }
 120                         else {
 121                                 string path;
 122                                 it = parameters.find("sabund");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 128                                 }
 129
 130                                 it = parameters.find("shared");
 131                                 //user has given a template file
 132                                 if(it != parameters.end()){
 133                                         path = m->hasPath(it->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 136                                 }
 137                         }
 138
 139                         //check for required parameters
 140                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 141                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 142                         else if (sabundfile == "not found") { sabundfile = "";  }
 143                         else { m->setSabundFile(sabundfile); }
 144
 145                         sharedfile = validParameter.validFile(parameters, "shared", true);
 146                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 147                         else if (sharedfile == "not found") { sharedfile = "";   }
 148                         else { m->setSharedFile(sharedfile); }
 149
 150                         string label = validParameter.validFile(parameters, "label", false);
 151                         if (label == "not found") { label = ""; }
 152                         else {
 153                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 154                                 else { allLines = 1;  }
 155                         }
 156
 157                         if ((sharedfile == "") && (sabundfile == "")) {
 158                                 //is there are current file available for either of these?
 159                                 //give priority to shared, then sabund
 160                                 //if there is a current shared file, use it
 161                                 sharedfile = m->getSharedFile();
 162                                 if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 163                                 else {
 164                                         sabundfile = m->getSabundFile();
 165                                         if (sabundfile != "") {  m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 166                                         else {
 167                                                 m->mothurOut("No valid current files. You must provide a sabund or shared file before you can use the catchall command."); m->mothurOutEndLine();
 168                                                 abort = true;
 169                                         }
 170                                 }
 171                         }
 172
 173                         //if the user changes the output directory command factory will send this info to us in the output parameter
 174                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 175                         if (outputDir == "not found"){
 176                                 if (sabundfile != "") {  outputDir = m->hasPath(sabundfile); }
 177                                 else { outputDir = m->hasPath(sharedfile); }
 178                         }
 179                 }
 180
 181         }
 182         catch(exception& e) {
 183                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
 184                 exit(1);
 185         }
 186 }
 187 /**************************************************************************************/
 188 int CatchAllCommand::execute() {
 189         try {
 190
 191                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 192
 193                 //get location of catchall
 194                 path = m->argv;
 195                 path = path.substr(0, (path.find_last_of("othur")-5));
 196                 path = m->getFullPathName(path);
 197
 198         if (m->debug) { m->mothurOut("[DEBUG]: mothur's path = " + path + "\n"); }
 199
 200                 savedOutputDir = outputDir;
 201                 string catchAllCommandExe = "";
 202         string catchAllTest = "";
 203                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 204                         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.
 205             catchAllTest = path + "CatchAllcmdL.exe";
 206                 #else
 207                         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.
 208             catchAllTest = path + "CatchAllcmdW.exe";
 209                 #endif
 210
 211         //test to make sure formatdb exists
 212                 ifstream in;
 213                 catchAllTest = m->getFullPathName(catchAllTest);
 214                 int ableToOpen = m->openInputFile(catchAllTest, in, "no error"); in.close();
 215                 if(ableToOpen == 1) {
 216             m->mothurOut(catchAllTest + " file does not exist. Checking path... \n");
 217             //check to see if uchime is in the path??
 218
 219             string programName = "CatchAllcmdW.exe";
 220 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 221             programName = "CatchAllcmdL.exe";
 222 #endif
 223             string cLocation = m->findProgramPath(programName);
 224
 225             ifstream in2;
 226             ableToOpen = m->openInputFile(cLocation, in2, "no error"); in2.close();
 227
 228             if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + cLocation + " file does not exist. mothur requires the catchall executable."); m->mothurOutEndLine();  return 0; }
 229             else {  m->mothurOut("Found catchall in your path, using " + cLocation + "\n"); catchAllTest = cLocation; }
 230         }
 231         catchAllTest = m->getFullPathName(catchAllTest);
 232
 233 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 234         catchAllCommandExe += "mono " + catchAllTest + " ";
 235 #else
 236         catchAllCommandExe += "\"" + catchAllTest + "\" ";
 237 #endif
 238
 239                 //prepare full output directory
 240                 outputDir = m->getFullPathName(outputDir);
 241
 242         if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + "\n[DEBUG]: outputDir = " + outputDir + "\n"); }
 243
 244                 vector<string> inputFileNames;
 245                 if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile);   }
 246                 else {  inputFileNames.push_back(sabundfile);  }
 247
 248                 for (int p = 0; p < inputFileNames.size(); p++) {
 249                         if (inputFileNames.size() > 1) {
 250                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 251                         }
 252
 253                         InputData input(inputFileNames[p], "sabund");
 254                         SAbundVector* sabund = input.getSAbundVector();
 255                         string lastLabel = sabund->getLabel();
 256
 257                         set<string> processedLabels;
 258                         set<string> userLabels = labels;
 259
 260                         string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + getOutputFileNameTag("summary");
 261                         summaryfilename = m->getFullPathName(summaryfilename);
 262
 263             if (m->debug) { m->mothurOut("[DEBUG]: Input File = " + inputFileNames[p] + ".\n[DEBUG]: inputdata address = " + toString(&input) + ".\n[DEBUG]: sabund address = " + toString(&sabund) + ".\n"); }
 264
 265                         ofstream out;
 266                         m->openOutputFile(summaryfilename, out);
 267
 268                         out << "label\tmodel\testimate\tlci\tuci" << endl;
 269
 270             if (m->debug) { string open = "no"; if (out.is_open()) { open = "yes"; } m->mothurOut("[DEBUG]: output stream is open = " + open + ".\n"); }
 271
 272                         //for each label the user selected
 273                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 274
 275
 276                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 277                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 278
 279                                                 //create catchall input file from mothur's inputfile
 280                                                 string filename = process(sabund, inputFileNames[p]);
 281                                                 string outputPath = m->getPathName(filename);
 282
 283                                                 //create system command
 284                                                 string catchAllCommand = "";
 285                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 286                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 287                                                 #else
 288                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 289                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 290                                                         //wrap entire string in ""
 291                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 292                                                 #endif
 293
 294                         if (m->debug) {  m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
 295
 296                                                 //run catchall
 297                                                 system(catchAllCommand.c_str());
 298
 299                         if (m->debug) { m->mothurOut("[DEBUG]: back from system call. Keeping file: " + filename + ".\n"); }
 300
 301                         if (!m->debug) { m->mothurRemove(filename); }
 302
 303
 304                                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 305                                                 if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 306
 307                                                 outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
 308                                                 outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
 309                                                 outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
 310                                                 outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));
 311
 312                         if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
 313
 314                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 315
 316                         if (m->debug) { m->mothurOut("[DEBUG]: Done creating summary file.\n"); }
 317
 318                                                 if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);   }  delete sabund;  return 0; }
 319
 320                                                 processedLabels.insert(sabund->getLabel());
 321                                                 userLabels.erase(sabund->getLabel());
 322                                 }
 323
 324                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 325                                                 string saveLabel = sabund->getLabel();
 326
 327                                                 delete sabund;
 328                                                 sabund = (input.getSAbundVector(lastLabel));
 329
 330                                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 331
 332
 333                                                 //create catchall input file from mothur's inputfile
 334                                                 string filename = process(sabund, inputFileNames[p]);
 335                                                 string outputPath = m->getPathName(filename);
 336
 337                                                 //create system command
 338                                                 string catchAllCommand = "";
 339                                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 340                                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 341                                                 #else
 342                                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 343                                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 344                                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 345                                                 #endif
 346
 347                         if (m->debug) {  m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
 348
 349                                                 //run catchall
 350                                                 system(catchAllCommand.c_str());
 351
 352                         if (m->debug) { m->mothurOut("[DEBUG]: back from system call. Keeping file: " + filename + ".\n"); }
 353
 354                         if (!m->debug) { m->mothurRemove(filename); }
 355
 356
 357                                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 358                                                 if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 359
 360                         outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
 361                         outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
 362                         outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
 363                         outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));
 364
 365
 366                         if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
 367
 368                                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 369
 370                         if (m->debug) { m->mothurOut("[DEBUG]: Done creating summary file.\n"); }
 371
 372                                                 if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);   }   delete sabund;  return 0; }
 373
 374                                                 processedLabels.insert(sabund->getLabel());
 375                                                 userLabels.erase(sabund->getLabel());
 376
 377                                                 //restore real lastlabel to save below
 378                                                 sabund->setLabel(saveLabel);
 379                                 }
 380
 381
 382                                 lastLabel = sabund->getLabel();
 383
 384                                 delete sabund;
 385                                 sabund = (input.getSAbundVector());
 386                         }
 387
 388                         //output error messages about any remaining user labels
 389                         set<string>::iterator it;
 390                         bool needToRun = false;
 391                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 392                                 m->mothurOut("Your file does not include the label " + *it);
 393                                 if (processedLabels.count(lastLabel) != 1) {
 394                                         m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 395                                         needToRun = true;
 396                                 }else {
 397                                         m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 398                                 }
 399                         }
 400
 401                         //run last label if you need to
 402                         if (needToRun == true)  {
 403                                 if (sabund != NULL) {   delete sabund;  }
 404                                 sabund = (input.getSAbundVector(lastLabel));
 405
 406                                 m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 407
 408                                 //create catchall input file from mothur's inputfile
 409                                 string filename = process(sabund, inputFileNames[p]);
 410                                 string outputPath = m->getPathName(filename);
 411
 412                                 //create system command
 413                                 string catchAllCommand = "";
 414                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 415                                         catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
 416                                 #else
 417                                         if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
 418                                         catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \""  + outputPath + "\" 1";
 419                                         catchAllCommand = "\"" + catchAllCommand + "\"";
 420                                 #endif
 421
 422                 if (m->debug) {  m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); }
 423
 424                                 //run catchall
 425                                 system(catchAllCommand.c_str());
 426
 427                 if (m->debug) { m->mothurOut("[DEBUG]: back from system call. Keeping file: " + filename + ".\n"); }
 428
 429                                 if (!m->debug) { m->mothurRemove(filename); }
 430
 431                                 filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 432                                 if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 433
 434                                 outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv"));
 435                 outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv"));
 436                 outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv"));
 437                 outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv"));                          if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); }
 438
 439                                 createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
 440
 441                 if (m->debug) { m->mothurOut("[DEBUG]: Done creating summary file.\n"); }
 442
 443                                 delete sabund;
 444                         }
 445
 446                         out.close();
 447
 448                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);        } return 0; }
 449
 450                 }
 451
 452                 if (sharedfile == "") {
 453                         string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
 454                         summaryfilename = m->getFullPathName(summaryfilename);
 455                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 456                 }else { //combine summaries
 457                         vector<string> sumNames;
 458                         for (int i = 0; i < inputFileNames.size(); i++) {
 459                                 sumNames.push_back(m->getFullPathName(outputDir + m->getRootName(m->getSimpleName(inputFileNames[i])) + "catchall.summary"));
 460                         }
 461                         string summaryfilename = combineSummmary(sumNames);
 462                         outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 463                 }
 464
 465                 m->mothurOutEndLine();
 466                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 467                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 468                 m->mothurOutEndLine();
 469
 470
 471                 return 0;
 472         }
 473         catch(exception& e) {
 474                 m->errorOut(e, "CatchAllCommand", "execute");
 475                 exit(1);
 476         }
 477 }
 478 //**********************************************************************************************************************
 479 string CatchAllCommand::process(SAbundVector* sabund, string file1) {
 480         try {
 481                 string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv";
 482                 filename = m->getFullPathName(filename);
 483
 484                 ofstream out;
 485                 m->openOutputFile(filename, out);
 486
 487         if (m->debug) { m->mothurOut("[DEBUG]: Creating " + filename + " file for catchall, shown below.\n\n"); }
 488
 489                 for (int i = 1; i <= sabund->getMaxRank(); i++) {
 490                         int temp = sabund->get(i);
 491
 492                         if (temp != 0) {
 493                                 out << i << "," << temp << endl;
 494                 if (m->debug) { m->mothurOut(toString(i) + "," + toString(temp) + "\n"); }
 495                         }
 496                 }
 497                 out.close();
 498
 499         if (m->debug) { m->mothurOut("[DEBUG]: Done creating " + filename + " file for catchall, shown above.\n\n"); }
 500
 501                 return filename;
 502
 503         }
 504         catch(exception& e) {
 505                 m->errorOut(e, "CatchAllCommand", "process");
 506                 exit(1);
 507         }
 508 }
 509 //*********************************************************************************************************************
 510 string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
 511         try {
 512
 513                 ofstream out;
 514                 string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
 515
 516                 //open combined file
 517                 m->openOutputFile(combineFileName, out);
 518
 519                 out << "label\tgroup\tmodel\testimate\tlci\tuci" << endl;
 520
 521                 //open each groups summary file
 522                 string newLabel = "";
 523                 int numLines = 0;
 524                 map<string, vector<string> > files;
 525                 for (int i=0; i<outputNames.size(); i++) {
 526                         vector<string> thisFilesLines;
 527
 528                         ifstream temp;
 529                         m->openInputFile(outputNames[i], temp);
 530
 531                         //read through first line - labels
 532                         m->getline(temp);
 533                         m->gobble(temp);
 534
 535                         //for each label
 536                         while (!temp.eof()) {
 537
 538                                 string thisLine = "";
 539                                 string tempLabel;
 540
 541                                 for (int j = 0; j < 5; j++) {
 542                                         temp >> tempLabel;
 543
 544                                         //save for later
 545                                         if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t";  }
 546                                         else{  thisLine += tempLabel + "\t";    }
 547                                 }
 548
 549                                 thisLine += "\n";
 550
 551                                 thisFilesLines.push_back(thisLine);
 552
 553                                 m->gobble(temp);
 554                         }
 555
 556                         files[outputNames[i]] = thisFilesLines;
 557
 558                         numLines = thisFilesLines.size();
 559
 560                         temp.close();
 561                         m->mothurRemove(outputNames[i]);
 562                 }
 563
 564                 //for each label
 565                 for (int k = 0; k < numLines; k++) {
 566
 567                         //grab summary data for each group
 568                         for (int i=0; i<outputNames.size(); i++) {
 569                                 out << files[outputNames[i]][k];
 570                         }
 571                 }
 572
 573
 574                 out.close();
 575
 576                 //return combine file name
 577                 return combineFileName;
 578
 579         }
 580         catch(exception& e) {
 581                 m->errorOut(e, "CatchAllCommand", "combineSummmary");
 582                 exit(1);
 583         }
 584 }
 585 //**********************************************************************************************************************
 586 int CatchAllCommand::createSummaryFile(string file1, string label, ofstream& out) {
 587         try {
 588
 589                 ifstream in;
 590                 int able = m->openInputFile(file1, in, "noerror");
 591
 592                 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; }
 593
 594                 if (!in.eof()) {
 595
 596                         string header = m->getline(in); m->gobble(in);
 597
 598                         int pos = header.find("Total Number of Observed Species =");
 599                         string numString = "";
 600
 601
 602                         if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); }
 603                         else {
 604                                 //pos will be the position of the T in total, so we want to count to the position of =
 605                                 pos += 34;
 606                                 char c=header[pos];
 607                                 while (c != ','){
 608                                         if (c != ' ') {
 609                                                 numString += c;
 610                                         }
 611                                         pos++;
 612                                         c=header[pos];
 613
 614                                         //sanity check
 615                                         if (pos > header.length()) { m->mothurOut("Cannot find number of OTUs in " + file1); m->mothurOutEndLine(); in.close(); return 0; }
 616                                 }
 617                         }
 618
 619                         string firstline = m->getline(in); m->gobble(in);
 620                         vector<string> values;
 621                         m->splitAtComma(firstline, values);
 622
 623                         values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 624
 625                         if (values.size() == 1) { //grab next line if firstline didn't have what you wanted
 626                                 string secondline = m->getline(in); m->gobble(in);
 627                                 values.clear();
 628                                 m->splitAtComma(secondline, values);
 629
 630                                 values.pop_back(); //last value is always a blank string since the last character in the line is always a ','
 631                         }
 632
 633                         if (values.size() == 1) { //still not what we wanted fill values with numOTUs
 634                                 values.resize(8, "");
 635                                 values[1] = "Sobs";
 636                                 values[4] = numString;
 637                                 values[6] = numString;
 638                                 values[7] = numString;
 639                         }
 640
 641                         if (values.size() < 8) { values.resize(8, ""); }
 642
 643                         out << label << '\t' << values[1] << '\t' << values[4] << '\t' << values[6] << '\t' << values[7] << endl;
 644                 }
 645
 646                 in.close();
 647
 648                 return 0;
 649
 650         }
 651         catch(exception& e) {
 652                 m->errorOut(e, "CatchAllCommand", "createSummaryFile");
 653                 exit(1);
 654         }
 655 }
 656 //**********************************************************************************************************************
 657 vector<string> CatchAllCommand::parseSharedFile(string filename) {
 658         try {
 659                 vector<string> filenames;
 660
 661                 //read first line
 662                 InputData input(filename, "sharedfile");
 663                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 664
 665                 string sharedFileRoot = outputDir + m->getRootName(m->getSimpleName(filename));
 666
 667                 //clears file before we start to write to it below
 668                 for (int i=0; i<lookup.size(); i++) {
 669                         m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
 670                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
 671                         groups.push_back(lookup[i]->getGroup());
 672                 }
 673
 674                 while(lookup[0] != NULL) {
 675
 676                         for (int i = 0; i < lookup.size(); i++) {
 677                                 SAbundVector sav = lookup[i]->getSAbundVector();
 678                                 ofstream out;
 679                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".sabund", out);
 680                                 sav.print(out);
 681                                 out.close();
 682                         }
 683
 684                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 685                         lookup = input.getSharedRAbundVectors();
 686                 }
 687
 688                 return filenames;
 689         }
 690         catch(exception& e) {
 691                 m->errorOut(e, "CatchAllCommand", "parseSharedFile");
 692                 exit(1);
 693         }
 694 }
 695 /**************************************************************************************/