rarefactcommand.cpp

   1 /*
   2  *  rarefactcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactcommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "nseqs.h"
  14 #include "chao1.h"
  15 #include "bootstrap.h"
  16 #include "simpson.h"
  17 #include "simpsoneven.h"
  18 #include "heip.h"
  19 #include "smithwilson.h"
  20 #include "invsimpson.h"
  21 #include "npshannon.h"
  22 #include "shannoneven.h"
  23 #include "shannon.h"
  24 #include "jackknife.h"
  25 #include "coverage.h"
  26
  27
  28 //**********************************************************************************************************************
  29 vector<string> RareFactCommand::setParameters(){
  30         try {
  31                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
  32                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(prabund);
  33                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(psabund);
  34                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
  35                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  36                 CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
  37                 CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
  38                 CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc);
  39                 CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
  40                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  41                 CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
  42                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  43                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  44
  45                 vector<string> myArray;
  46                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  47                 return myArray;
  48         }
  49         catch(exception& e) {
  50                 m->errorOut(e, "RareFactCommand", "setParameters");
  51                 exit(1);
  52         }
  53 }
  54 //**********************************************************************************************************************
  55 string RareFactCommand::getHelpString(){
  56         try {
  57                 ValidCalculators validCalculator;
  58                 string helpString = "";
  59                 helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors, groupmode and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
  60                 helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
  61                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  62                 helpString += "The rarefaction.single command should be in the following format: \n";
  63                 helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
  64                 helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n";
  65                 helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n";
  66                 validCalculator.printCalc("rarefaction");
  67                 helpString += "If you are running rarefaction.single with a shared file and would like your results collated in one file, set groupmode=t. (Default=true).\n";
  68                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  69                 helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
  70                 return helpString;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "RareFactCommand", "getHelpString");
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78 string RareFactCommand::getOutputPattern(string type) {
  79     try {
  80         string pattern = "";
  81         if (type == "rarefaction") {  pattern =  "[filename],rarefaction"; }
  82         else if (type == "r_chao") {  pattern =  "[filename],r_chao"; }
  83         else if (type == "r_ace") {  pattern =  "[filename],r_ace"; }
  84         else if (type == "r_jack") {  pattern =  "[filename],r_jack"; }
  85         else if (type == "r_shannon") {  pattern =  "[filename],r_shannon"; }
  86         else if (type == "r_shannoneven") {  pattern =  "[filename],r_shannoneven"; }
  87         else if (type == "r_smithwilson") {  pattern =  "[filename],r_smithwilson"; }
  88         else if (type == "r_npshannon") {  pattern =  "[filename],r_npshannon"; }
  89         else if (type == "r_simpson") {  pattern =  "[filename],r_simpson"; }
  90         else if (type == "r_simpsoneven") {  pattern =  "[filename],r_simpsoneven"; }
  91         else if (type == "r_invsimpson") {  pattern =  "[filename],r_invsimpson"; }
  92         else if (type == "r_bootstrap") {  pattern =  "[filename],r_bootstrap"; }
  93         else if (type == "r_coverage") {  pattern =  "[filename],r_coverage"; }
  94         else if (type == "r_nseqs") {  pattern =  "[filename],r_nseqs"; }
  95         else if (type == "r_heip") {  pattern =  "[filename],r_heip"; }
  96         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  97
  98         return pattern;
  99     }
 100     catch(exception& e) {
 101         m->errorOut(e, "RareFactCommand", "getOutputPattern");
 102         exit(1);
 103     }
 104 }
 105 //**********************************************************************************************************************
 106 RareFactCommand::RareFactCommand(){
 107         try {
 108                 abort = true; calledHelp = true;
 109                 setParameters();
 110                 vector<string> tempOutNames;
 111                 outputTypes["rarefaction"] = tempOutNames;
 112                 outputTypes["r_chao"] = tempOutNames;
 113                 outputTypes["r_ace"] = tempOutNames;
 114                 outputTypes["r_jack"] = tempOutNames;
 115                 outputTypes["r_shannon"] = tempOutNames;
 116                 outputTypes["r_shannoneven"] = tempOutNames;
 117                 outputTypes["r_heip"] = tempOutNames;
 118                 outputTypes["r_smithwilson"] = tempOutNames;
 119                 outputTypes["r_npshannon"] = tempOutNames;
 120                 outputTypes["r_simpson"] = tempOutNames;
 121                 outputTypes["r_simpsoneven"] = tempOutNames;
 122                 outputTypes["r_invsimpson"] = tempOutNames;
 123                 outputTypes["r_bootstrap"] = tempOutNames;
 124                 outputTypes["r_coverage"] = tempOutNames;
 125                 outputTypes["r_nseqs"] = tempOutNames;
 126         }
 127         catch(exception& e) {
 128                 m->errorOut(e, "RareFactCommand", "RareFactCommand");
 129                 exit(1);
 130         }
 131 }
 132 //**********************************************************************************************************************
 133 RareFactCommand::RareFactCommand(string option)  {
 134         try {
 135                 abort = false; calledHelp = false;
 136                 allLines = 1;
 137
 138                 //allow user to run help
 139                 if(option == "help") { help(); abort = true; calledHelp = true; }
 140                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 141
 142                 else {
 143                         vector<string> myArray = setParameters();
 144
 145                         OptionParser parser(option);
 146                         map<string,string> parameters = parser.getParameters();
 147                         map<string,string>::iterator it;
 148
 149                         ValidParameters validParameter;
 150
 151                         //check to make sure all parameters are valid for command
 152                         for (it = parameters.begin(); it != parameters.end(); it++) {
 153                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 154                         }
 155
 156                         //initialize outputTypes
 157                         vector<string> tempOutNames;
 158                         outputTypes["rarefaction"] = tempOutNames;
 159                         outputTypes["r_chao"] = tempOutNames;
 160                         outputTypes["r_ace"] = tempOutNames;
 161                         outputTypes["r_jack"] = tempOutNames;
 162                         outputTypes["r_shannon"] = tempOutNames;
 163                         outputTypes["r_shannoneven"] = tempOutNames;
 164                         outputTypes["r_heip"] = tempOutNames;
 165                         outputTypes["r_smithwilson"] = tempOutNames;
 166                         outputTypes["r_npshannon"] = tempOutNames;
 167                         outputTypes["r_simpson"] = tempOutNames;
 168                         outputTypes["r_simpsoneven"] = tempOutNames;
 169                         outputTypes["r_invsimpson"] = tempOutNames;
 170                         outputTypes["r_bootstrap"] = tempOutNames;
 171                         outputTypes["r_coverage"] = tempOutNames;
 172                         outputTypes["r_nseqs"] = tempOutNames;
 173
 174                         //if the user changes the input directory command factory will send this info to us in the output parameter
 175                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 176                         if (inputDir == "not found"){   inputDir = "";          }
 177                         else {
 178                                 string path;
 179                                 it = parameters.find("shared");
 180                                 //user has given a template file
 181                                 if(it != parameters.end()){
 182                                         path = m->hasPath(it->second);
 183                                         //if the user has not given a path then, add inputdir. else leave path alone.
 184                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 185                                 }
 186
 187                                 it = parameters.find("rabund");
 188                                 //user has given a template file
 189                                 if(it != parameters.end()){
 190                                         path = m->hasPath(it->second);
 191                                         //if the user has not given a path then, add inputdir. else leave path alone.
 192                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 193                                 }
 194
 195                                 it = parameters.find("sabund");
 196                                 //user has given a template file
 197                                 if(it != parameters.end()){
 198                                         path = m->hasPath(it->second);
 199                                         //if the user has not given a path then, add inputdir. else leave path alone.
 200                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 201                                 }
 202
 203                                 it = parameters.find("list");
 204                                 //user has given a template file
 205                                 if(it != parameters.end()){
 206                                         path = m->hasPath(it->second);
 207                                         //if the user has not given a path then, add inputdir. else leave path alone.
 208                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 209                                 }
 210                         }
 211
 212                         //check for required parameters
 213                         listfile = validParameter.validFile(parameters, "list", true);
 214                         if (listfile == "not open") { listfile = ""; abort = true; }
 215                         else if (listfile == "not found") { listfile = ""; }
 216                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 217
 218                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 219                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 220                         else if (sabundfile == "not found") { sabundfile = ""; }
 221                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 222
 223                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 224                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 225                         else if (rabundfile == "not found") { rabundfile = ""; }
 226                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 227
 228                         sharedfile = validParameter.validFile(parameters, "shared", true);
 229                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 230                         else if (sharedfile == "not found") { sharedfile = ""; }
 231                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 232
 233                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 234                                 //is there are current file available for any of these?
 235                                 //give priority to shared, then list, then rabund, then sabund
 236                                 //if there is a current shared file, use it
 237                                 sharedfile = m->getSharedFile();
 238                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 239                                 else {
 240                                         listfile = m->getListFile();
 241                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 242                                         else {
 243                                                 rabundfile = m->getRabundFile();
 244                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 245                                                 else {
 246                                                         sabundfile = m->getSabundFile();
 247                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 248                                                         else {
 249                                                                 m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine();
 250                                                                 abort = true;
 251                                                         }
 252                                                 }
 253                                         }
 254                                 }
 255                         }
 256
 257                         //if the user changes the output directory command factory will send this info to us in the output parameter
 258                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 259
 260                         //check for optional parameter and set defaults
 261                         // ...at some point should added some additional type checking...
 262                         label = validParameter.validFile(parameters, "label", false);
 263                         if (label == "not found") { label = ""; }
 264                         else {
 265                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 266                                 else { allLines = 1;  }
 267                         }
 268
 269                         calc = validParameter.validFile(parameters, "calc", false);
 270                         if (calc == "not found") { calc = "sobs";  }
 271                         else {
 272                                  if (calc == "default")  {  calc = "sobs";  }
 273                         }
 274                         m->splitAtDash(calc, Estimators);
 275                         if (m->inUsersGroups("citation", Estimators)) {
 276                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 277                                 //remove citation from list of calcs
 278                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 279                         }
 280
 281                         string temp;
 282                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 283                         m->mothurConvert(temp, freq);
 284
 285                         temp = validParameter.validFile(parameters, "abund", false);                    if (temp == "not found") { temp = "10"; }
 286                         m->mothurConvert(temp, abund);
 287
 288                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
 289                         m->mothurConvert(temp, nIters);
 290
 291                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 292                         m->setProcessors(temp);
 293                         m->mothurConvert(temp, processors);
 294
 295                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
 296                         groupMode = m->isTrue(temp);
 297                 }
 298
 299         }
 300         catch(exception& e) {
 301                 m->errorOut(e, "RareFactCommand", "RareFactCommand");
 302                 exit(1);
 303         }
 304 }
 305 //**********************************************************************************************************************
 306
 307 int RareFactCommand::execute(){
 308         try {
 309
 310                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 311
 312         map<string, set<int> > labelToEnds;
 313                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 314                 else {  inputFileNames = parseSharedFile(sharedfile, labelToEnds);  format = "rabund"; }
 315
 316         if (m->control_pressed) { return 0; }
 317
 318                 map<int, string> file2Group; //index in outputNames[i] -> group
 319                 for (int p = 0; p < inputFileNames.size(); p++) {
 320
 321                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
 322
 323                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  m->clearGroups();  return 0; }
 324
 325                         if (inputFileNames.size() > 1) {
 326                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 327                         }
 328                         int i;
 329                         ValidCalculators validCalculator;
 330
 331             map<string, string> variables;
 332             variables["[filename]"] = fileNameRoot;
 333
 334                         for (i=0; i<Estimators.size(); i++) {
 335                                 if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) {
 336                                         if (Estimators[i] == "sobs") {
 337                                                 rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(getOutputFileName("rarefaction",variables))));
 338                                                 outputNames.push_back(getOutputFileName("rarefaction",variables)); outputTypes["rarefaction"].push_back(getOutputFileName("rarefaction",variables));
 339                                         }else if (Estimators[i] == "chao") {
 340                                                 rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("r_chao",variables))));
 341                                                 outputNames.push_back(getOutputFileName("r_chao",variables)); outputTypes["r_chao"].push_back(getOutputFileName("r_chao",variables));
 342                                         }else if (Estimators[i] == "ace") {
 343                                                 if(abund < 5)
 344                                                         abund = 10;
 345                                                 rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("r_ace",variables))));
 346                                                 outputNames.push_back(getOutputFileName("r_ace",variables)); outputTypes["r_ace"].push_back(getOutputFileName("r_ace",variables));
 347                                         }else if (Estimators[i] == "jack") {
 348                                                 rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("r_jack",variables))));
 349                                                 outputNames.push_back(getOutputFileName("r_jack",variables)); outputTypes["r_jack"].push_back(getOutputFileName("r_jack",variables));
 350                                         }else if (Estimators[i] == "shannon") {
 351                                                 rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("r_shannon",variables))));
 352                                                 outputNames.push_back(getOutputFileName("r_shannon",variables)); outputTypes["r_shannon"].push_back(getOutputFileName("r_shannon",variables));
 353                                         }else if (Estimators[i] == "shannoneven") {
 354                                                 rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(getOutputFileName("r_shannoneven",variables))));
 355                                                 outputNames.push_back(getOutputFileName("r_shannoneven",variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannoneven",variables));
 356                                         }else if (Estimators[i] == "heip") {
 357                                                 rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables))));
 358                                                 outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables));
 359                                         }else if (Estimators[i] == "smithwilson") {
 360                                                 rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables))));
 361                                                 outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables));
 362                                         }else if (Estimators[i] == "npshannon") {
 363                                                 rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(getOutputFileName("r_npshannon",variables))));
 364                                                 outputNames.push_back(getOutputFileName("r_npshannon",variables)); outputTypes["r_npshannon"].push_back(getOutputFileName("r_npshannon",variables));
 365                                         }else if (Estimators[i] == "simpson") {
 366                                                 rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("r_simpson",variables))));
 367                                                 outputNames.push_back(getOutputFileName("r_simpson",variables)); outputTypes["r_simpson"].push_back(getOutputFileName("r_simpson",variables));
 368                                         }else if (Estimators[i] == "simpsoneven") {
 369                                                 rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(getOutputFileName("r_simpsoneven",variables))));
 370                                                 outputNames.push_back(getOutputFileName("r_simpsoneven",variables)); outputTypes["r_simpsoneven"].push_back(getOutputFileName("r_simpsoneven",variables));
 371                                         }else if (Estimators[i] == "invsimpson") {
 372                                                 rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("r_invsimpson",variables))));
 373                                                 outputNames.push_back(getOutputFileName("r_invsimpson",variables)); outputTypes["r_invsimpson"].push_back(getOutputFileName("r_invsimpson",variables));
 374                                         }else if (Estimators[i] == "bootstrap") {
 375                                                 rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(getOutputFileName("r_bootstrap",variables))));
 376                                                 outputNames.push_back(getOutputFileName("r_bootstrap",variables)); outputTypes["r_bootstrap"].push_back(getOutputFileName("r_bootstrap",variables));
 377                                         }else if (Estimators[i] == "coverage") {
 378                                                 rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(getOutputFileName("r_coverage",variables))));
 379                                                 outputNames.push_back(getOutputFileName("r_coverage",variables)); outputTypes["r_coverage"].push_back(getOutputFileName("r_coverage",variables));
 380                                         }else if (Estimators[i] == "nseqs") {
 381                                                 rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(getOutputFileName("r_nseqs",variables))));
 382                                                 outputNames.push_back(getOutputFileName("r_nseqs",variables)); outputTypes["r_nseqs"].push_back(getOutputFileName("r_nseqs",variables));
 383                                         }
 384                     if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
 385                                 }
 386                         }
 387
 388
 389                         //if the users entered no valid calculators don't execute command
 390                         if (rDisplays.size() == 0) { for(int i=0;i<rDisplays.size();i++){       delete rDisplays[i];    }  return 0; }
 391
 392                         input = new InputData(inputFileNames[p], format);
 393                         order = input->getOrderVector();
 394                         string lastLabel = order->getLabel();
 395
 396                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 397                         set<string> processedLabels;
 398                         set<string> userLabels = labels;
 399
 400                         if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 401
 402                         //as long as you are not at the end of the file or done wih the lines you want
 403                         while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 404
 405                                 if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;  delete order;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 406
 407
 408                                 if(allLines == 1 || labels.count(order->getLabel()) == 1){
 409
 410                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 411                     map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
 412                     set<int> ends;
 413                     if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
 414                                         rCurve = new Rarefact(order, rDisplays, processors, ends);
 415                                         rCurve->getCurve(freq, nIters);
 416                                         delete rCurve;
 417
 418                                         processedLabels.insert(order->getLabel());
 419                                         userLabels.erase(order->getLabel());
 420                                 }
 421
 422                                 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 423                                         string saveLabel = order->getLabel();
 424
 425                                         delete order;
 426                                         order = (input->getOrderVector(lastLabel));
 427
 428                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 429                                         map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
 430                     set<int> ends;
 431                     if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
 432                                         rCurve = new Rarefact(order, rDisplays, processors, ends);
 433
 434                                         rCurve->getCurve(freq, nIters);
 435                                         delete rCurve;
 436
 437                                         processedLabels.insert(order->getLabel());
 438                                         userLabels.erase(order->getLabel());
 439
 440                                         //restore real lastlabel to save below
 441                                         order->setLabel(saveLabel);
 442                                 }
 443
 444                                 lastLabel = order->getLabel();
 445
 446                                 delete order;
 447                                 order = (input->getOrderVector());
 448                         }
 449
 450                         if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;   for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 451
 452                         //output error messages about any remaining user labels
 453                         set<string>::iterator it;
 454                         bool needToRun = false;
 455                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 456                                 m->mothurOut("Your file does not include the label " + *it);
 457                                 if (processedLabels.count(lastLabel) != 1) {
 458                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 459                                         needToRun = true;
 460                                 }else {
 461                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 462                                 }
 463                         }
 464
 465                         if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){  delete rDisplays[i];    }  delete input;   for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 466
 467                         //run last label if you need to
 468                         if (needToRun == true)  {
 469                                 if (order != NULL) {    delete order;   }
 470                                 order = (input->getOrderVector(lastLabel));
 471
 472                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 473                                 map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
 474                 set<int> ends;
 475                 if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
 476                 rCurve = new Rarefact(order, rDisplays, processors, ends);
 477
 478                                 rCurve->getCurve(freq, nIters);
 479                                 delete rCurve;
 480
 481                                 delete order;
 482                         }
 483
 484
 485                         for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 486                         rDisplays.clear();
 487                         delete input;
 488                 }
 489
 490
 491                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 492
 493                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 494                 if ((sharedfile != "") && (groupMode)) {   outputNames = createGroupFile(outputNames, file2Group);  }
 495
 496                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 497
 498                 m->mothurOutEndLine();
 499                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 500                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 501                 m->mothurOutEndLine();
 502
 503                 return 0;
 504         }
 505         catch(exception& e) {
 506                 m->errorOut(e, "RareFactCommand", "execute");
 507                 exit(1);
 508         }
 509 }
 510 //**********************************************************************************************************************
 511 vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map<int, string> file2Group) {
 512         try {
 513
 514                 vector<string> newFileNames;
 515
 516                 //find different types of files
 517                 map<string, map<string, string> > typesFiles;
 518         map<string, vector< vector<string> > > fileLabels; //combofile name to labels. each label is a vector because it may be unique lci hci.
 519         vector<string> groupNames;
 520                 for (int i = 0; i < outputNames.size(); i++) {
 521
 522                         string extension = m->getExtension(outputNames[i]);
 523             string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
 524                         m->mothurRemove(combineFileName); //remove old file
 525
 526                         ifstream in;
 527                         m->openInputFile(outputNames[i], in);
 528
 529                         string labels = m->getline(in);
 530
 531                         istringstream iss (labels,istringstream::in);
 532             string newLabel = ""; vector<string> theseLabels;
 533             while(!iss.eof()) {  iss >> newLabel; m->gobble(iss); theseLabels.push_back(newLabel); }
 534             vector< vector<string> > allLabels;
 535             vector<string> thisSet; thisSet.push_back(theseLabels[0]); allLabels.push_back(thisSet); thisSet.clear(); //makes "numSampled" its own grouping
 536             for (int j = 1; j < theseLabels.size()-1; j++) {
 537                 if (theseLabels[j+1] == "lci") {
 538                     thisSet.push_back(theseLabels[j]);
 539                     thisSet.push_back(theseLabels[j+1]);
 540                     thisSet.push_back(theseLabels[j+2]);
 541                     j++; j++;
 542                 }else{ //no lci or hci for this calc.
 543                     thisSet.push_back(theseLabels[j]);
 544                 }
 545                 allLabels.push_back(thisSet);
 546                 thisSet.clear();
 547             }
 548             fileLabels[combineFileName] = allLabels;
 549
 550             map<string, map<string, string> >::iterator itfind = typesFiles.find(extension);
 551             if (itfind != typesFiles.end()) {
 552                 (itfind->second)[outputNames[i]] = file2Group[i];
 553             }else {
 554                 map<string, string> temp;
 555                 temp[outputNames[i]] = file2Group[i];
 556                 typesFiles[extension] = temp;
 557             }
 558             if (!(m->inUsersGroups(file2Group[i], groupNames))) {  groupNames.push_back(file2Group[i]); }
 559                 }
 560
 561                 //for each type create a combo file
 562
 563                 for (map<string, map<string, string> >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) {
 564
 565                         ofstream out;
 566                         string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first;
 567                         m->openOutputFileAppend(combineFileName, out);
 568                         newFileNames.push_back(combineFileName);
 569                         map<string, string> thisTypesFiles = it->second; //it->second maps filename to group
 570             set<int> numSampledSet;
 571
 572                         //open each type summary file
 573                         map<string, map<int, vector< vector<string> > > > files; //maps file name to lines in file
 574                         int maxLines = 0;
 575                         for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
 576
 577                 string thisfilename = itFileNameGroup->first;
 578                 string group = itFileNameGroup->second;
 579
 580                                 ifstream temp;
 581                                 m->openInputFile(thisfilename, temp);
 582
 583                                 //read through first line - labels
 584                                 m->getline(temp);       m->gobble(temp);
 585
 586                                 map<int, vector< vector<string> > > thisFilesLines;
 587                                 while (!temp.eof()){
 588                     int numSampled = 0;
 589                     temp >> numSampled; m->gobble(temp);
 590
 591                     vector< vector<string> > theseReads;
 592                     vector<string> thisSet; thisSet.push_back(toString(numSampled)); theseReads.push_back(thisSet); thisSet.clear();
 593                     for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A
 594                         vector<string> reads;
 595                         string next = "";
 596                         for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels
 597                             temp >> next; m->gobble(temp);
 598                             reads.push_back(next);
 599                         }
 600                         theseReads.push_back(reads);
 601                     }
 602                     thisFilesLines[numSampled] = theseReads;
 603                     m->gobble(temp);
 604
 605                     numSampledSet.insert(numSampled);
 606                                 }
 607
 608                                 files[group] = thisFilesLines;
 609
 610                                 //save longest file for below
 611                                 if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); }
 612
 613                                 temp.close();
 614                                 m->mothurRemove(thisfilename);
 615                         }
 616
 617             //output new labels line
 618             out << fileLabels[combineFileName][0][0] << '\t';
 619             for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A
 620                 for (int n = 0; n < groupNames.size(); n++) { // for each group
 621                     for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels
 622                         out << fileLabels[combineFileName][k][l] << '-' << groupNames[n] << '\t';
 623                     }
 624                 }
 625             }
 626                         out << endl;
 627
 628                         //for each label
 629                         for (set<int>::iterator itNumSampled = numSampledSet.begin(); itNumSampled != numSampledSet.end(); itNumSampled++) {
 630
 631                 out << (*itNumSampled) << '\t';
 632
 633                 if (m->control_pressed) { break; }
 634
 635                 for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //each chunk
 636                                     //grab data for each group
 637                     for (map<string, map<int, vector< vector<string> > > >::iterator itFileNameGroup = files.begin(); itFileNameGroup != files.end(); itFileNameGroup++) {
 638
 639                         string group = itFileNameGroup->first;
 640
 641                         map<int, vector< vector<string> > >::iterator itLine = files[group].find(*itNumSampled);
 642                         if (itLine != files[group].end()) {
 643                             for (int l = 0; l < (itLine->second)[k].size(); l++) {
 644                                 out << (itLine->second)[k][l] << '\t';
 645
 646                             }
 647                         }else {
 648                             for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) {
 649                                 out << "NA" << '\t';
 650                             }
 651                         }
 652                     }
 653                 }
 654                 out << endl;
 655                         }
 656                         out.close();
 657                 }
 658
 659                 //return combine file name
 660                 return newFileNames;
 661
 662         }
 663         catch(exception& e) {
 664                 m->errorOut(e, "RareFactCommand", "createGroupFile");
 665                 exit(1);
 666         }
 667 }
 668 //**********************************************************************************************************************
 669 vector<string> RareFactCommand::parseSharedFile(string filename, map<string, set<int> >& label2Ends) {
 670         try {
 671                 vector<string> filenames;
 672
 673                 map<string, ofstream*> filehandles;
 674                 map<string, ofstream*>::iterator it3;
 675
 676                 input = new InputData(filename, "sharedfile");
 677                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 678
 679                 string sharedFileRoot = m->getRootName(filename);
 680
 681                 //clears file before we start to write to it below
 682                 for (int i=0; i<lookup.size(); i++) {
 683                         m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 684                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 685                 }
 686
 687                 ofstream* temp;
 688                 for (int i=0; i<lookup.size(); i++) {
 689                         temp = new ofstream;
 690                         filehandles[lookup[i]->getGroup()] = temp;
 691                         groups.push_back(lookup[i]->getGroup());
 692                 }
 693
 694                 while(lookup[0] != NULL) {
 695
 696                         for (int i = 0; i < lookup.size(); i++) {
 697                                 RAbundVector rav = lookup[i]->getRAbundVector();
 698                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 699                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 700                                 (*(filehandles[lookup[i]->getGroup()])).close();
 701                 label2Ends[lookup[i]->getLabel()].insert(rav.getNumSeqs());
 702                         }
 703
 704                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 705                         lookup = input->getSharedRAbundVectors();
 706                 }
 707
 708                 //free memory
 709                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 710                         delete it3->second;
 711                 }
 712
 713                 delete input;
 714                 m->clearGroups();
 715
 716                 return filenames;
 717         }
 718         catch(exception& e) {
 719                 m->errorOut(e, "RareFactCommand", "parseSharedFile");
 720                 exit(1);
 721         }
 722 }
 723 //**********************************************************************************************************************
 724
 725
 726