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 #include "shannonrange.h"
  27
  28
  29 //**********************************************************************************************************************
  30 vector<string> RareFactCommand::setParameters(){
  31         try {
  32                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
  33                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(prabund);
  34                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(psabund);
  35                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
  36                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  37                 CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
  38                 CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
  39                 CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-shannonrange", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc);
  40                 CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
  41         CommandParameter palpha("alpha", "Multiple", "0-1-2", "1", "", "", "","",false,false,true); parameters.push_back(palpha);
  42                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  43                 CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
  44                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  45                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  46
  47                 vector<string> myArray;
  48                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  49                 return myArray;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "RareFactCommand", "setParameters");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 string RareFactCommand::getHelpString(){
  58         try {
  59                 ValidCalculators validCalculator;
  60                 string helpString = "";
  61                 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";
  62                 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";
  63                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  64                 helpString += "The rarefaction.single command should be in the following format: \n";
  65                 helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
  66                 helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n";
  67                 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";
  68         helpString += "The alpha parameter is used to set the alpha value for the shannonrange calculator.\n";
  69                 validCalculator.printCalc("rarefaction");
  70                 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";
  71                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  72                 helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
  73                 return helpString;
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "RareFactCommand", "getHelpString");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81 string RareFactCommand::getOutputPattern(string type) {
  82     try {
  83         string pattern = "";
  84         if (type == "rarefaction") {  pattern =  "[filename],rarefaction"; }
  85         else if (type == "r_chao") {  pattern =  "[filename],r_chao"; }
  86         else if (type == "r_ace") {  pattern =  "[filename],r_ace"; }
  87         else if (type == "r_jack") {  pattern =  "[filename],r_jack"; }
  88         else if (type == "r_shannon") {  pattern =  "[filename],r_shannon"; }
  89         else if (type == "r_shannoneven") {  pattern =  "[filename],r_shannoneven"; }
  90         else if (type == "r_smithwilson") {  pattern =  "[filename],r_smithwilson"; }
  91         else if (type == "r_npshannon") {  pattern =  "[filename],r_npshannon"; }
  92         else if (type == "r_shannonrange"){  pattern =  "[filename],r_shannonrange";    }
  93         else if (type == "r_simpson") {  pattern =  "[filename],r_simpson"; }
  94         else if (type == "r_simpsoneven") {  pattern =  "[filename],r_simpsoneven"; }
  95         else if (type == "r_invsimpson") {  pattern =  "[filename],r_invsimpson"; }
  96         else if (type == "r_bootstrap") {  pattern =  "[filename],r_bootstrap"; }
  97         else if (type == "r_coverage") {  pattern =  "[filename],r_coverage"; }
  98         else if (type == "r_nseqs") {  pattern =  "[filename],r_nseqs"; }
  99         else if (type == "r_heip") {  pattern =  "[filename],r_heip"; }
 100         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
 101
 102         return pattern;
 103     }
 104     catch(exception& e) {
 105         m->errorOut(e, "RareFactCommand", "getOutputPattern");
 106         exit(1);
 107     }
 108 }
 109 //**********************************************************************************************************************
 110 RareFactCommand::RareFactCommand(){
 111         try {
 112                 abort = true; calledHelp = true;
 113                 setParameters();
 114                 vector<string> tempOutNames;
 115                 outputTypes["rarefaction"] = tempOutNames;
 116                 outputTypes["r_chao"] = tempOutNames;
 117                 outputTypes["r_ace"] = tempOutNames;
 118                 outputTypes["r_jack"] = tempOutNames;
 119                 outputTypes["r_shannon"] = tempOutNames;
 120                 outputTypes["r_shannoneven"] = tempOutNames;
 121         outputTypes["r_shannonrange"] = tempOutNames;
 122                 outputTypes["r_heip"] = tempOutNames;
 123                 outputTypes["r_smithwilson"] = tempOutNames;
 124                 outputTypes["r_npshannon"] = tempOutNames;
 125                 outputTypes["r_simpson"] = tempOutNames;
 126                 outputTypes["r_simpsoneven"] = tempOutNames;
 127                 outputTypes["r_invsimpson"] = tempOutNames;
 128                 outputTypes["r_bootstrap"] = tempOutNames;
 129                 outputTypes["r_coverage"] = tempOutNames;
 130                 outputTypes["r_nseqs"] = tempOutNames;
 131         }
 132         catch(exception& e) {
 133                 m->errorOut(e, "RareFactCommand", "RareFactCommand");
 134                 exit(1);
 135         }
 136 }
 137 //**********************************************************************************************************************
 138 RareFactCommand::RareFactCommand(string option)  {
 139         try {
 140                 abort = false; calledHelp = false;
 141                 allLines = 1;
 142
 143                 //allow user to run help
 144                 if(option == "help") { help(); abort = true; calledHelp = true; }
 145                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 146
 147                 else {
 148                         vector<string> myArray = setParameters();
 149
 150                         OptionParser parser(option);
 151                         map<string,string> parameters = parser.getParameters();
 152                         map<string,string>::iterator it;
 153
 154                         ValidParameters validParameter;
 155
 156                         //check to make sure all parameters are valid for command
 157                         for (it = parameters.begin(); it != parameters.end(); it++) {
 158                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 159                         }
 160
 161                         //initialize outputTypes
 162                         vector<string> tempOutNames;
 163                         outputTypes["rarefaction"] = tempOutNames;
 164                         outputTypes["r_chao"] = tempOutNames;
 165                         outputTypes["r_ace"] = tempOutNames;
 166                         outputTypes["r_jack"] = tempOutNames;
 167                         outputTypes["r_shannon"] = tempOutNames;
 168                         outputTypes["r_shannoneven"] = tempOutNames;
 169             outputTypes["r_shannonrange"] = tempOutNames;
 170                         outputTypes["r_heip"] = tempOutNames;
 171                         outputTypes["r_smithwilson"] = tempOutNames;
 172                         outputTypes["r_npshannon"] = tempOutNames;
 173                         outputTypes["r_simpson"] = tempOutNames;
 174                         outputTypes["r_simpsoneven"] = tempOutNames;
 175                         outputTypes["r_invsimpson"] = tempOutNames;
 176                         outputTypes["r_bootstrap"] = tempOutNames;
 177                         outputTypes["r_coverage"] = tempOutNames;
 178                         outputTypes["r_nseqs"] = tempOutNames;
 179
 180                         //if the user changes the input directory command factory will send this info to us in the output parameter
 181                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 182                         if (inputDir == "not found"){   inputDir = "";          }
 183                         else {
 184                                 string path;
 185                                 it = parameters.find("shared");
 186                                 //user has given a template file
 187                                 if(it != parameters.end()){
 188                                         path = m->hasPath(it->second);
 189                                         //if the user has not given a path then, add inputdir. else leave path alone.
 190                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 191                                 }
 192
 193                                 it = parameters.find("rabund");
 194                                 //user has given a template file
 195                                 if(it != parameters.end()){
 196                                         path = m->hasPath(it->second);
 197                                         //if the user has not given a path then, add inputdir. else leave path alone.
 198                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 199                                 }
 200
 201                                 it = parameters.find("sabund");
 202                                 //user has given a template file
 203                                 if(it != parameters.end()){
 204                                         path = m->hasPath(it->second);
 205                                         //if the user has not given a path then, add inputdir. else leave path alone.
 206                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 207                                 }
 208
 209                                 it = parameters.find("list");
 210                                 //user has given a template file
 211                                 if(it != parameters.end()){
 212                                         path = m->hasPath(it->second);
 213                                         //if the user has not given a path then, add inputdir. else leave path alone.
 214                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 215                                 }
 216                         }
 217
 218                         //check for required parameters
 219                         listfile = validParameter.validFile(parameters, "list", true);
 220                         if (listfile == "not open") { listfile = ""; abort = true; }
 221                         else if (listfile == "not found") { listfile = ""; }
 222                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 223
 224                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 225                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 226                         else if (sabundfile == "not found") { sabundfile = ""; }
 227                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 228
 229                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 230                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 231                         else if (rabundfile == "not found") { rabundfile = ""; }
 232                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 233
 234                         sharedfile = validParameter.validFile(parameters, "shared", true);
 235                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 236                         else if (sharedfile == "not found") { sharedfile = ""; }
 237                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 238
 239                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 240                                 //is there are current file available for any of these?
 241                                 //give priority to shared, then list, then rabund, then sabund
 242                                 //if there is a current shared file, use it
 243                                 sharedfile = m->getSharedFile();
 244                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 245                                 else {
 246                                         listfile = m->getListFile();
 247                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 248                                         else {
 249                                                 rabundfile = m->getRabundFile();
 250                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 251                                                 else {
 252                                                         sabundfile = m->getSabundFile();
 253                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 254                                                         else {
 255                                                                 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();
 256                                                                 abort = true;
 257                                                         }
 258                                                 }
 259                                         }
 260                                 }
 261                         }
 262
 263                         //if the user changes the output directory command factory will send this info to us in the output parameter
 264                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 265
 266                         //check for optional parameter and set defaults
 267                         // ...at some point should added some additional type checking...
 268                         label = validParameter.validFile(parameters, "label", false);
 269                         if (label == "not found") { label = ""; }
 270                         else {
 271                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 272                                 else { allLines = 1;  }
 273                         }
 274
 275                         calc = validParameter.validFile(parameters, "calc", false);
 276                         if (calc == "not found") { calc = "sobs";  }
 277                         else {
 278                                  if (calc == "default")  {  calc = "sobs";  }
 279                         }
 280                         m->splitAtDash(calc, Estimators);
 281                         if (m->inUsersGroups("citation", Estimators)) {
 282                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 283                                 //remove citation from list of calcs
 284                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 285                         }
 286
 287                         string temp;
 288                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 289                         m->mothurConvert(temp, freq);
 290
 291                         temp = validParameter.validFile(parameters, "abund", false);                    if (temp == "not found") { temp = "10"; }
 292                         m->mothurConvert(temp, abund);
 293
 294                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
 295                         m->mothurConvert(temp, nIters);
 296
 297                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 298                         m->setProcessors(temp);
 299                         m->mothurConvert(temp, processors);
 300
 301             temp = validParameter.validFile(parameters, "alpha", false);                if (temp == "not found") { temp = "1"; }
 302                         m->mothurConvert(temp, alpha);
 303
 304             if ((alpha != 0) && (alpha != 1) && (alpha != 2)) { m->mothurOut("[ERROR]: Not a valid alpha value. Valid values are 0, 1 and 2."); m->mothurOutEndLine(); abort=true; }
 305
 306                         temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "T"; }
 307                         groupMode = m->isTrue(temp);
 308                 }
 309
 310         }
 311         catch(exception& e) {
 312                 m->errorOut(e, "RareFactCommand", "RareFactCommand");
 313                 exit(1);
 314         }
 315 }
 316 //**********************************************************************************************************************
 317
 318 int RareFactCommand::execute(){
 319         try {
 320
 321                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 322
 323         map<string, set<int> > labelToEnds;
 324                 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile);  }
 325                 else {  inputFileNames = parseSharedFile(sharedfile, labelToEnds);  format = "rabund"; }
 326
 327         if (m->control_pressed) { return 0; }
 328
 329                 map<int, string> file2Group; //index in outputNames[i] -> group
 330                 for (int p = 0; p < inputFileNames.size(); p++) {
 331
 332                         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
 333
 334                         if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  m->clearGroups();  return 0; }
 335
 336                         if (inputFileNames.size() > 1) {
 337                                 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
 338                         }
 339                         int i;
 340                         ValidCalculators validCalculator;
 341
 342             map<string, string> variables;
 343             variables["[filename]"] = fileNameRoot;
 344
 345                         for (i=0; i<Estimators.size(); i++) {
 346                                 if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) {
 347                                         if (Estimators[i] == "sobs") {
 348                                                 rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(getOutputFileName("rarefaction",variables))));
 349                                                 outputNames.push_back(getOutputFileName("rarefaction",variables)); outputTypes["rarefaction"].push_back(getOutputFileName("rarefaction",variables));
 350                                         }else if (Estimators[i] == "chao") {
 351                                                 rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("r_chao",variables))));
 352                                                 outputNames.push_back(getOutputFileName("r_chao",variables)); outputTypes["r_chao"].push_back(getOutputFileName("r_chao",variables));
 353                                         }else if (Estimators[i] == "ace") {
 354                                                 if(abund < 5)
 355                                                         abund = 10;
 356                                                 rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("r_ace",variables))));
 357                                                 outputNames.push_back(getOutputFileName("r_ace",variables)); outputTypes["r_ace"].push_back(getOutputFileName("r_ace",variables));
 358                                         }else if (Estimators[i] == "jack") {
 359                                                 rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("r_jack",variables))));
 360                                                 outputNames.push_back(getOutputFileName("r_jack",variables)); outputTypes["r_jack"].push_back(getOutputFileName("r_jack",variables));
 361                                         }else if (Estimators[i] == "shannon") {
 362                                                 rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("r_shannon",variables))));
 363                                                 outputNames.push_back(getOutputFileName("r_shannon",variables)); outputTypes["r_shannon"].push_back(getOutputFileName("r_shannon",variables));
 364                                         }else if (Estimators[i] == "shannoneven") {
 365                                                 rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(getOutputFileName("r_shannoneven",variables))));
 366                                                 outputNames.push_back(getOutputFileName("r_shannoneven",variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannoneven",variables));
 367                                         }else if (Estimators[i] == "heip") {
 368                                                 rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables))));
 369                                                 outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables));
 370                     }else if (Estimators[i] == "r_shannonrange") {
 371                         rDisplays.push_back(new RareDisplay(new RangeShannon(alpha), new ThreeColumnFile(getOutputFileName("r_shannonrange", variables))));
 372                         outputNames.push_back(getOutputFileName("r_shannonrange", variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannonrange", variables));
 373                                         }else if (Estimators[i] == "smithwilson") {
 374                                                 rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables))));
 375                                                 outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables));
 376                                         }else if (Estimators[i] == "npshannon") {
 377                                                 rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(getOutputFileName("r_npshannon",variables))));
 378                                                 outputNames.push_back(getOutputFileName("r_npshannon",variables)); outputTypes["r_npshannon"].push_back(getOutputFileName("r_npshannon",variables));
 379                                         }else if (Estimators[i] == "simpson") {
 380                                                 rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("r_simpson",variables))));
 381                                                 outputNames.push_back(getOutputFileName("r_simpson",variables)); outputTypes["r_simpson"].push_back(getOutputFileName("r_simpson",variables));
 382                                         }else if (Estimators[i] == "simpsoneven") {
 383                                                 rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(getOutputFileName("r_simpsoneven",variables))));
 384                                                 outputNames.push_back(getOutputFileName("r_simpsoneven",variables)); outputTypes["r_simpsoneven"].push_back(getOutputFileName("r_simpsoneven",variables));
 385                                         }else if (Estimators[i] == "invsimpson") {
 386                                                 rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("r_invsimpson",variables))));
 387                                                 outputNames.push_back(getOutputFileName("r_invsimpson",variables)); outputTypes["r_invsimpson"].push_back(getOutputFileName("r_invsimpson",variables));
 388                                         }else if (Estimators[i] == "bootstrap") {
 389                                                 rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(getOutputFileName("r_bootstrap",variables))));
 390                                                 outputNames.push_back(getOutputFileName("r_bootstrap",variables)); outputTypes["r_bootstrap"].push_back(getOutputFileName("r_bootstrap",variables));
 391                                         }else if (Estimators[i] == "coverage") {
 392                                                 rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(getOutputFileName("r_coverage",variables))));
 393                                                 outputNames.push_back(getOutputFileName("r_coverage",variables)); outputTypes["r_coverage"].push_back(getOutputFileName("r_coverage",variables));
 394                                         }else if (Estimators[i] == "nseqs") {
 395                                                 rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(getOutputFileName("r_nseqs",variables))));
 396                                                 outputNames.push_back(getOutputFileName("r_nseqs",variables)); outputTypes["r_nseqs"].push_back(getOutputFileName("r_nseqs",variables));
 397                                         }
 398                     if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
 399                                 }
 400                         }
 401
 402
 403                         //if the users entered no valid calculators don't execute command
 404                         if (rDisplays.size() == 0) { for(int i=0;i<rDisplays.size();i++){       delete rDisplays[i];    }  return 0; }
 405
 406                         input = new InputData(inputFileNames[p], format);
 407                         order = input->getOrderVector();
 408                         string lastLabel = order->getLabel();
 409
 410                         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 411                         set<string> processedLabels;
 412                         set<string> userLabels = labels;
 413
 414                         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; }
 415
 416                         //as long as you are not at the end of the file or done wih the lines you want
 417                         while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 418
 419                                 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; }
 420
 421
 422                                 if(allLines == 1 || labels.count(order->getLabel()) == 1){
 423
 424                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 425                     map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
 426                     set<int> ends;
 427                     if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
 428                                         rCurve = new Rarefact(order, rDisplays, processors, ends);
 429                                         rCurve->getCurve(freq, nIters);
 430                                         delete rCurve;
 431
 432                                         processedLabels.insert(order->getLabel());
 433                                         userLabels.erase(order->getLabel());
 434                                 }
 435
 436                                 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 437                                         string saveLabel = order->getLabel();
 438
 439                                         delete order;
 440                                         order = (input->getOrderVector(lastLabel));
 441
 442                                         m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 443                                         map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
 444                     set<int> ends;
 445                     if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
 446                                         rCurve = new Rarefact(order, rDisplays, processors, ends);
 447
 448                                         rCurve->getCurve(freq, nIters);
 449                                         delete rCurve;
 450
 451                                         processedLabels.insert(order->getLabel());
 452                                         userLabels.erase(order->getLabel());
 453
 454                                         //restore real lastlabel to save below
 455                                         order->setLabel(saveLabel);
 456                                 }
 457
 458                                 lastLabel = order->getLabel();
 459
 460                                 delete order;
 461                                 order = (input->getOrderVector());
 462                         }
 463
 464                         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; }
 465
 466                         //output error messages about any remaining user labels
 467                         set<string>::iterator it;
 468                         bool needToRun = false;
 469                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 470                                 m->mothurOut("Your file does not include the label " + *it);
 471                                 if (processedLabels.count(lastLabel) != 1) {
 472                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 473                                         needToRun = true;
 474                                 }else {
 475                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 476                                 }
 477                         }
 478
 479                         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; }
 480
 481                         //run last label if you need to
 482                         if (needToRun == true)  {
 483                                 if (order != NULL) {    delete order;   }
 484                                 order = (input->getOrderVector(lastLabel));
 485
 486                                 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 487                                 map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
 488                 set<int> ends;
 489                 if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
 490                 rCurve = new Rarefact(order, rDisplays, processors, ends);
 491
 492                                 rCurve->getCurve(freq, nIters);
 493                                 delete rCurve;
 494
 495                                 delete order;
 496                         }
 497
 498
 499                         for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 500                         rDisplays.clear();
 501                         delete input;
 502                 }
 503
 504
 505                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 506
 507                 //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 508                 if ((sharedfile != "") && (groupMode)) {   outputNames = createGroupFile(outputNames, file2Group);  }
 509
 510                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 511
 512                 m->mothurOutEndLine();
 513                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 514                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 515                 m->mothurOutEndLine();
 516
 517                 return 0;
 518         }
 519         catch(exception& e) {
 520                 m->errorOut(e, "RareFactCommand", "execute");
 521                 exit(1);
 522         }
 523 }
 524 //**********************************************************************************************************************
 525 vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map<int, string> file2Group) {
 526         try {
 527
 528                 vector<string> newFileNames;
 529
 530                 //find different types of files
 531                 map<string, map<string, string> > typesFiles;
 532         map<string, vector< vector<string> > > fileLabels; //combofile name to labels. each label is a vector because it may be unique lci hci.
 533         vector<string> groupNames;
 534                 for (int i = 0; i < outputNames.size(); i++) {
 535
 536                         string extension = m->getExtension(outputNames[i]);
 537             string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
 538                         m->mothurRemove(combineFileName); //remove old file
 539
 540                         ifstream in;
 541                         m->openInputFile(outputNames[i], in);
 542
 543                         string labels = m->getline(in);
 544
 545                         istringstream iss (labels,istringstream::in);
 546             string newLabel = ""; vector<string> theseLabels;
 547             while(!iss.eof()) {  iss >> newLabel; m->gobble(iss); theseLabels.push_back(newLabel); }
 548             vector< vector<string> > allLabels;
 549             vector<string> thisSet; thisSet.push_back(theseLabels[0]); allLabels.push_back(thisSet); thisSet.clear(); //makes "numSampled" its own grouping
 550             for (int j = 1; j < theseLabels.size()-1; j++) {
 551                 if (theseLabels[j+1] == "lci") {
 552                     thisSet.push_back(theseLabels[j]);
 553                     thisSet.push_back(theseLabels[j+1]);
 554                     thisSet.push_back(theseLabels[j+2]);
 555                     j++; j++;
 556                 }else{ //no lci or hci for this calc.
 557                     thisSet.push_back(theseLabels[j]);
 558                 }
 559                 allLabels.push_back(thisSet);
 560                 thisSet.clear();
 561             }
 562             fileLabels[combineFileName] = allLabels;
 563
 564             map<string, map<string, string> >::iterator itfind = typesFiles.find(extension);
 565             if (itfind != typesFiles.end()) {
 566                 (itfind->second)[outputNames[i]] = file2Group[i];
 567             }else {
 568                 map<string, string> temp;
 569                 temp[outputNames[i]] = file2Group[i];
 570                 typesFiles[extension] = temp;
 571             }
 572             if (!(m->inUsersGroups(file2Group[i], groupNames))) {  groupNames.push_back(file2Group[i]); }
 573                 }
 574
 575                 //for each type create a combo file
 576
 577                 for (map<string, map<string, string> >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) {
 578
 579                         ofstream out;
 580                         string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first;
 581                         m->openOutputFileAppend(combineFileName, out);
 582                         newFileNames.push_back(combineFileName);
 583                         map<string, string> thisTypesFiles = it->second; //it->second maps filename to group
 584             set<int> numSampledSet;
 585
 586                         //open each type summary file
 587                         map<string, map<int, vector< vector<string> > > > files; //maps file name to lines in file
 588                         int maxLines = 0;
 589                         for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
 590
 591                 string thisfilename = itFileNameGroup->first;
 592                 string group = itFileNameGroup->second;
 593
 594                                 ifstream temp;
 595                                 m->openInputFile(thisfilename, temp);
 596
 597                                 //read through first line - labels
 598                                 m->getline(temp);       m->gobble(temp);
 599
 600                                 map<int, vector< vector<string> > > thisFilesLines;
 601                                 while (!temp.eof()){
 602                     int numSampled = 0;
 603                     temp >> numSampled; m->gobble(temp);
 604
 605                     vector< vector<string> > theseReads;
 606                     vector<string> thisSet; thisSet.push_back(toString(numSampled)); theseReads.push_back(thisSet); thisSet.clear();
 607                     for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A
 608                         vector<string> reads;
 609                         string next = "";
 610                         for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels
 611                             temp >> next; m->gobble(temp);
 612                             reads.push_back(next);
 613                         }
 614                         theseReads.push_back(reads);
 615                     }
 616                     thisFilesLines[numSampled] = theseReads;
 617                     m->gobble(temp);
 618
 619                     numSampledSet.insert(numSampled);
 620                                 }
 621
 622                                 files[group] = thisFilesLines;
 623
 624                                 //save longest file for below
 625                                 if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); }
 626
 627                                 temp.close();
 628                                 m->mothurRemove(thisfilename);
 629                         }
 630
 631             //output new labels line
 632             out << fileLabels[combineFileName][0][0] << '\t';
 633             for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A
 634                 for (int n = 0; n < groupNames.size(); n++) { // for each group
 635                     for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels
 636                         out << fileLabels[combineFileName][k][l] << '-' << groupNames[n] << '\t';
 637                     }
 638                 }
 639             }
 640                         out << endl;
 641
 642                         //for each label
 643                         for (set<int>::iterator itNumSampled = numSampledSet.begin(); itNumSampled != numSampledSet.end(); itNumSampled++) {
 644
 645                 out << (*itNumSampled) << '\t';
 646
 647                 if (m->control_pressed) { break; }
 648
 649                 for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //each chunk
 650                                     //grab data for each group
 651                     for (map<string, map<int, vector< vector<string> > > >::iterator itFileNameGroup = files.begin(); itFileNameGroup != files.end(); itFileNameGroup++) {
 652
 653                         string group = itFileNameGroup->first;
 654
 655                         map<int, vector< vector<string> > >::iterator itLine = files[group].find(*itNumSampled);
 656                         if (itLine != files[group].end()) {
 657                             for (int l = 0; l < (itLine->second)[k].size(); l++) {
 658                                 out << (itLine->second)[k][l] << '\t';
 659
 660                             }
 661                         }else {
 662                             for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) {
 663                                 out << "NA" << '\t';
 664                             }
 665                         }
 666                     }
 667                 }
 668                 out << endl;
 669                         }
 670                         out.close();
 671                 }
 672
 673                 //return combine file name
 674                 return newFileNames;
 675
 676         }
 677         catch(exception& e) {
 678                 m->errorOut(e, "RareFactCommand", "createGroupFile");
 679                 exit(1);
 680         }
 681 }
 682 //**********************************************************************************************************************
 683 vector<string> RareFactCommand::parseSharedFile(string filename, map<string, set<int> >& label2Ends) {
 684         try {
 685                 vector<string> filenames;
 686
 687                 map<string, ofstream*> filehandles;
 688                 map<string, ofstream*>::iterator it3;
 689
 690                 input = new InputData(filename, "sharedfile");
 691                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 692
 693                 string sharedFileRoot = m->getRootName(filename);
 694
 695                 //clears file before we start to write to it below
 696                 for (int i=0; i<lookup.size(); i++) {
 697                         m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 698                         filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 699                 }
 700
 701                 ofstream* temp;
 702                 for (int i=0; i<lookup.size(); i++) {
 703                         temp = new ofstream;
 704                         filehandles[lookup[i]->getGroup()] = temp;
 705                         groups.push_back(lookup[i]->getGroup());
 706                 }
 707
 708                 while(lookup[0] != NULL) {
 709
 710                         for (int i = 0; i < lookup.size(); i++) {
 711                                 RAbundVector rav = lookup[i]->getRAbundVector();
 712                                 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
 713                                 rav.print(*(filehandles[lookup[i]->getGroup()]));
 714                                 (*(filehandles[lookup[i]->getGroup()])).close();
 715                 label2Ends[lookup[i]->getLabel()].insert(rav.getNumSeqs());
 716                         }
 717
 718                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 719                         lookup = input->getSharedRAbundVectors();
 720                 }
 721
 722                 //free memory
 723                 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
 724                         delete it3->second;
 725                 }
 726
 727                 delete input;
 728                 m->clearGroups();
 729
 730                 return filenames;
 731         }
 732         catch(exception& e) {
 733                 m->errorOut(e, "RareFactCommand", "parseSharedFile");
 734                 exit(1);
 735         }
 736 }
 737 //**********************************************************************************************************************
 738
 739
 740