removerarecommand.cpp

   1 /*
   2  *  removerarecommand.cpp
   3  *  mothur
   4  *
   5  *  Created by westcott on 1/21/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "removerarecommand.h"
  11 #include "sequence.hpp"
  12 #include "groupmap.h"
  13 #include "sharedutilities.h"
  14 #include "inputdata.h"
  15
  16 //**********************************************************************************************************************
  17 vector<string> RemoveRareCommand::setParameters(){
  18         try {
  19                 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
  20                 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
  21                 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
  22                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
  23                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
  24                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  25                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  26                 CommandParameter pnseqs("nseqs", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnseqs);
  27                 CommandParameter pbygroup("bygroup", "Boolean", "", "f", "", "", "",false,true); parameters.push_back(pbygroup);
  28                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  29                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  30
  31                 vector<string> myArray;
  32                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  33                 return myArray;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "RemoveRareCommand", "setParameters");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 string RemoveRareCommand::getHelpString(){
  42         try {
  43                 string helpString = "";
  44                 helpString += "The remove.rare command parameters are list, rabund, sabund, shared, group, label, groups, bygroup and nseqs.\n";
  45                 helpString += "The remove.rare command reads one of the following file types: list, rabund, sabund or shared file. It outputs a new file after removing the rare otus.\n";
  46                 helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.  Default=all. You may separate group names with dashes.\n";
  47                 helpString += "The label parameter is used to analyze specific labels in your input. default=all. You may separate label names with dashes.\n";
  48                 helpString += "The bygroup parameter is only valid with the shared file. default=f, meaning remove any OTU that has nseqs or fewer sequences across all groups.\n";
  49                 helpString += "bygroups=T means remove any OTU that has nseqs or fewer sequences in each group (if groupA has 1 sequence and group B has 100 sequences in OTUZ and nseqs=1, then set the groupA count for OTUZ to 0 and keep groupB's count at 100.) \n";
  50                 helpString += "The nseqs parameter allows you to set the cutoff for an otu to be deemed rare. It is required.\n";
  51                 helpString += "The remove.rare command should be in the following format: remove.rare(shared=yourSharedFile, nseqs=yourRareCutoff).\n";
  52                 helpString += "Example remove.rare(shared=amazon.fn.shared, nseqs=2).\n";
  53                 helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedFile).\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "RemoveRareCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 string RemoveRareCommand::getOutputFileNameTag(string type, string inputName=""){
  63         try {
  64         string outputFileName = "";
  65                 map<string, vector<string> >::iterator it;
  66
  67         //is this a type this command creates
  68         it = outputTypes.find(type);
  69         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  70         else {
  71             if (type == "rabund")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
  72             else if (type == "sabund")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
  73             else if (type == "shared")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  74             else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  75             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  76             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  77         }
  78         return outputFileName;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "RemoveRareCommand", "getOutputFileNameTag");
  82                 exit(1);
  83         }
  84 }
  85
  86 //**********************************************************************************************************************
  87 RemoveRareCommand::RemoveRareCommand(){
  88         try {
  89                 abort = true; calledHelp = true;
  90                 setParameters();
  91                 vector<string> tempOutNames;
  92                 outputTypes["rabund"] = tempOutNames;
  93                 outputTypes["sabund"] = tempOutNames;
  94                 outputTypes["list"] = tempOutNames;
  95                 outputTypes["group"] = tempOutNames;
  96                 outputTypes["shared"] = tempOutNames;
  97         }
  98         catch(exception& e) {
  99                 m->errorOut(e, "RemoveRareCommand", "RemoveRareCommand");
 100                 exit(1);
 101         }
 102 }
 103 //**********************************************************************************************************************
 104 RemoveRareCommand::RemoveRareCommand(string option)  {
 105         try {
 106                 abort = false; calledHelp = false;
 107                 allLines = 1;
 108
 109                 //allow user to run help
 110                 if(option == "help") { help(); abort = true; calledHelp = true; }
 111                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 112
 113                 else {
 114                         vector<string> myArray = setParameters();
 115
 116                         OptionParser parser(option);
 117                         map<string,string> parameters = parser.getParameters();
 118
 119                         ValidParameters validParameter;
 120                         map<string,string>::iterator it;
 121
 122                         //check to make sure all parameters are valid for command
 123                         for (it = parameters.begin(); it != parameters.end(); it++) {
 124                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 125                         }
 126
 127                         //initialize outputTypes
 128                         vector<string> tempOutNames;
 129                         outputTypes["rabund"] = tempOutNames;
 130                         outputTypes["sabund"] = tempOutNames;
 131                         outputTypes["list"] = tempOutNames;
 132                         outputTypes["group"] = tempOutNames;
 133                         outputTypes["shared"] = tempOutNames;
 134
 135                         //if the user changes the output directory command factory will send this info to us in the output parameter
 136                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 137
 138                         //if the user changes the input directory command factory will send this info to us in the output parameter
 139                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 140                         if (inputDir == "not found"){   inputDir = "";          }
 141                         else {
 142                                 string path;
 143                                 it = parameters.find("list");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 149                                 }
 150
 151                                 it = parameters.find("group");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 157                                 }
 158
 159                                 it = parameters.find("sabund");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 165                                 }
 166
 167                                 it = parameters.find("rabund");
 168                                 //user has given a template file
 169                                 if(it != parameters.end()){
 170                                         path = m->hasPath(it->second);
 171                                         //if the user has not given a path then, add inputdir. else leave path alone.
 172                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 173                                 }
 174
 175                                 it = parameters.find("shared");
 176                                 //user has given a template file
 177                                 if(it != parameters.end()){
 178                                         path = m->hasPath(it->second);
 179                                         //if the user has not given a path then, add inputdir. else leave path alone.
 180                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 181                                 }
 182                         }
 183
 184
 185                         //check for file parameters
 186                         listfile = validParameter.validFile(parameters, "list", true);
 187                         if (listfile == "not open") { abort = true; }
 188                         else if (listfile == "not found") {  listfile = "";  }
 189                         else { m->setListFile(listfile); }
 190
 191                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 192                         if (sabundfile == "not open") { abort = true; }
 193                         else if (sabundfile == "not found") {  sabundfile = "";  }
 194                         else { m->setSabundFile(sabundfile); }
 195
 196                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 197                         if (rabundfile == "not open") { abort = true; }
 198                         else if (rabundfile == "not found") {  rabundfile = "";  }
 199                         else { m->setRabundFile(rabundfile); }
 200
 201                         groupfile = validParameter.validFile(parameters, "group", true);
 202                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 203                         else if (groupfile == "not found") {  groupfile = "";  }
 204                         else { m->setGroupFile(groupfile); }
 205
 206                         sharedfile = validParameter.validFile(parameters, "shared", true);
 207                         if (sharedfile == "not open") { sharedfile = "";  abort = true; }
 208                         else if (sharedfile == "not found") {  sharedfile = "";  }
 209                         else { m->setSharedFile(sharedfile); }
 210
 211                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 212                                 //is there are current file available for any of these?
 213                                 //give priority to shared, then list, then rabund, then sabund
 214                                 //if there is a current shared file, use it
 215                                 sharedfile = m->getSharedFile();
 216                                 if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 217                                 else {
 218                                         listfile = m->getListFile();
 219                                         if (listfile != "") {  m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 220                                         else {
 221                                                 rabundfile = m->getRabundFile();
 222                                                 if (rabundfile != "") {  m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 223                                                 else {
 224                                                         sabundfile = m->getSabundFile();
 225                                                         if (sabundfile != "") {  m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 226                                                         else {
 227                                                                 m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file."); m->mothurOutEndLine();
 228                                                                 abort = true;
 229                                                         }
 230                                                 }
 231                                         }
 232                                 }
 233                         }
 234
 235                         groups = validParameter.validFile(parameters, "groups", false);
 236                         if (groups == "not found") { groups = "all"; }
 237                         m->splitAtDash(groups, Groups);
 238
 239                         label = validParameter.validFile(parameters, "label", false);
 240                         if (label == "not found") { label = ""; }
 241                         else {
 242                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 243                                 else { allLines = 1;  }
 244                         }
 245
 246                         string temp = validParameter.validFile(parameters, "nseqs", false);
 247                         if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
 248                         else { m->mothurConvert(temp, nseqs); }
 249
 250                         temp = validParameter.validFile(parameters, "bygroup", false);   if (temp == "not found") { temp = "f"; }
 251                         byGroup = m->isTrue(temp);
 252
 253                         if (byGroup && (sharedfile == "")) { m->mothurOut("The byGroup parameter is only valid with a shared file."); m->mothurOutEndLine(); }
 254
 255                         if ((groupfile != "") && (listfile == "")) { m->mothurOut("A groupfile is only valid with a list file."); m->mothurOutEndLine(); groupfile = ""; }
 256                 }
 257
 258         }
 259         catch(exception& e) {
 260                 m->errorOut(e, "RemoveRareCommand", "RemoveRareCommand");
 261                 exit(1);
 262         }
 263 }
 264 //**********************************************************************************************************************
 265
 266 int RemoveRareCommand::execute(){
 267         try {
 268
 269                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 270
 271                 if (m->control_pressed) { return 0; }
 272
 273                 //read through the correct file and output lines you want to keep
 274                 if (sabundfile != "")           {               processSabund();        }
 275                 if (rabundfile != "")           {               processRabund();        }
 276                 if (listfile != "")                     {               processList();          }
 277                 if (sharedfile != "")           {               processShared();        }
 278
 279                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 280
 281                 if (outputNames.size() != 0) {
 282                         m->mothurOutEndLine();
 283                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 284                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 285                         m->mothurOutEndLine();
 286
 287                         //set rabund file as new current rabundfile
 288                         string current = "";
 289                         itTypes = outputTypes.find("rabund");
 290                         if (itTypes != outputTypes.end()) {
 291                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 292                         }
 293
 294                         itTypes = outputTypes.find("sabund");
 295                         if (itTypes != outputTypes.end()) {
 296                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 297                         }
 298
 299                         itTypes = outputTypes.find("group");
 300                         if (itTypes != outputTypes.end()) {
 301                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 302                         }
 303
 304                         itTypes = outputTypes.find("list");
 305                         if (itTypes != outputTypes.end()) {
 306                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 307                         }
 308
 309                         itTypes = outputTypes.find("shared");
 310                         if (itTypes != outputTypes.end()) {
 311                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 312                         }
 313                 }
 314
 315                 return 0;
 316         }
 317
 318         catch(exception& e) {
 319                 m->errorOut(e, "RemoveRareCommand", "execute");
 320                 exit(1);
 321         }
 322 }
 323
 324 //**********************************************************************************************************************
 325 int RemoveRareCommand::processList(){
 326         try {
 327                 string thisOutputDir = outputDir;
 328                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 329                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 330                 string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 331                 ofstream out, outGroup;
 332                 m->openOutputFile(outputFileName, out);
 333
 334                 bool wroteSomething = false;
 335
 336                 //you must provide a label because the names in the listfile need to be consistent
 337                 string thisLabel = "";
 338                 if (allLines) { m->mothurOut("For the listfile you must select one label, using first label in your listfile."); m->mothurOutEndLine(); }
 339                 else if (labels.size() > 1) { m->mothurOut("For the listfile you must select one label, using " + (*labels.begin()) + "."); m->mothurOutEndLine(); thisLabel = *labels.begin(); }
 340                 else { thisLabel = *labels.begin(); }
 341
 342                 InputData input(listfile, "list");
 343                 ListVector* list = input.getListVector();
 344
 345                 //get first one or the one we want
 346                 if (thisLabel != "") {
 347                         //use smart distancing
 348                         set<string> userLabels; userLabels.insert(thisLabel);
 349                         set<string> processedLabels;
 350                         string lastLabel = list->getLabel();
 351                         while((list != NULL) && (userLabels.size() != 0)) {
 352                                 if(userLabels.count(list->getLabel()) == 1){
 353                                         processedLabels.insert(list->getLabel());
 354                                         userLabels.erase(list->getLabel());
 355                                         break;
 356                                 }
 357
 358                                 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 359                                         processedLabels.insert(list->getLabel());
 360                                         userLabels.erase(list->getLabel());
 361                                         delete list;
 362                                         list = input.getListVector(lastLabel);
 363                                         break;
 364                                 }
 365                                 lastLabel = list->getLabel();
 366                                 delete list;
 367                                 list = input.getListVector();
 368                         }
 369                         if (userLabels.size() != 0) {
 370                                 m->mothurOut("Your file does not include the label " + thisLabel + ". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 371                                 list = input.getListVector(lastLabel);
 372                         }
 373                 }
 374
 375                 //if groupfile is given then use it
 376                 GroupMap* groupMap;
 377                 if (groupfile != "") {
 378                         groupMap = new GroupMap(groupfile); groupMap->readMap();
 379                         SharedUtil util;
 380                         vector<string> namesGroups = groupMap->getNamesOfGroups();
 381                         util.setGroups(Groups, namesGroups);
 382                         m->openOutputFile(outputGroupFileName, outGroup);
 383                 }
 384
 385
 386                 if (list != NULL) {
 387                         //make a new list vector
 388                         ListVector newList;
 389                         newList.setLabel(list->getLabel());
 390
 391                         //for each bin
 392                         for (int i = 0; i < list->getNumBins(); i++) {
 393                                 if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close();  m->mothurRemove(outputFileName);  return 0; }
 394
 395                                 //parse out names that are in accnos file
 396                                 string binnames = list->get(i);
 397                                 vector<string> names;
 398                                 string saveBinNames = binnames;
 399                                 m->splitAtComma(binnames, names);
 400
 401                                 vector<string> newGroupFile;
 402                                 if (groupfile != "") {
 403                                         vector<string> newNames;
 404                                         saveBinNames = "";
 405                                         for(int k = 0; k < names.size(); k++) {
 406                                                 string group = groupMap->getGroup(names[k]);
 407
 408                                                 if (m->inUsersGroups(group, Groups)) {
 409                                                         newGroupFile.push_back(names[k] + "\t" + group);
 410
 411                                                         newNames.push_back(names[k]);
 412                                                         saveBinNames += names[k] + ",";
 413                                                 }
 414                                         }
 415                                         names = newNames;
 416                                         saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1);
 417                                 }
 418
 419                                 if (names.size() > nseqs) { //keep bin
 420                                         newList.push_back(saveBinNames);
 421                                         for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; }
 422                                 }
 423                         }
 424
 425                         //print new listvector
 426                         if (newList.getNumBins() != 0) {
 427                                 wroteSomething = true;
 428                                 newList.print(out);
 429                         }
 430                 }
 431
 432                 out.close();
 433                 if (groupfile != "") { outGroup.close(); outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName); }
 434
 435                 if (wroteSomething == false) {  m->mothurOut("Your file contains only rare sequences."); m->mothurOutEndLine();  }
 436                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 437
 438                 return 0;
 439         }
 440         catch(exception& e) {
 441                 m->errorOut(e, "RemoveRareCommand", "processList");
 442                 exit(1);
 443         }
 444 }
 445 //**********************************************************************************************************************
 446 int RemoveRareCommand::processSabund(){
 447         try {
 448                 string thisOutputDir = outputDir;
 449                 if (outputDir == "") {  thisOutputDir += m->hasPath(sabundfile);  }
 450                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile);
 451                 outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
 452
 453                 ofstream out;
 454                 m->openOutputFile(outputFileName, out);
 455
 456                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 457                 InputData input(sabundfile, "sabund");
 458                 SAbundVector* sabund = input.getSAbundVector();
 459                 string lastLabel = sabund->getLabel();
 460                 set<string> processedLabels;
 461                 set<string> userLabels = labels;
 462
 463                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 464
 465                         if (m->control_pressed) { delete sabund; out.close(); return 0; }
 466
 467                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 468
 469                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 470                                 processedLabels.insert(sabund->getLabel());
 471                                 userLabels.erase(sabund->getLabel());
 472
 473                                 if (sabund->getMaxRank() > nseqs) {
 474                                         for(int i = 1; i <=nseqs; i++) {  sabund->set(i, 0); }
 475                                 }else { sabund->clear(); }
 476
 477                                 if (sabund->getNumBins() > 0) { sabund->print(out); }
 478                         }
 479
 480                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 481                                 string saveLabel = sabund->getLabel();
 482
 483                                 delete sabund;
 484                                 sabund = input.getSAbundVector(lastLabel);
 485
 486                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 487                                 processedLabels.insert(sabund->getLabel());
 488                                 userLabels.erase(sabund->getLabel());
 489
 490                                 if (sabund->getMaxRank() > nseqs) {
 491                                         for(int i = 1; i <=nseqs; i++) {  sabund->set(i, 0); }
 492                                 }else { sabund->clear(); }
 493
 494                                 if (sabund->getNumBins() > 0) { sabund->print(out); }
 495
 496                                 //restore real lastlabel to save below
 497                                 sabund->setLabel(saveLabel);
 498                         }
 499
 500                         lastLabel = sabund->getLabel();
 501
 502                         delete sabund;
 503                         sabund = input.getSAbundVector();
 504                 }
 505
 506                 if (m->control_pressed) {  out.close(); return 0; }
 507
 508                 //output error messages about any remaining user labels
 509                 set<string>::iterator it;
 510                 bool needToRun = false;
 511                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 512                         m->mothurOut("Your file does not include the label " + *it);
 513                         if (processedLabels.count(lastLabel) != 1) {
 514                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 515                                 needToRun = true;
 516                         }else {
 517                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 518                         }
 519                 }
 520
 521                 //run last label if you need to
 522                 if (needToRun == true)  {
 523                         if (sabund != NULL) {   delete sabund;  }
 524                         sabund = input.getSAbundVector(lastLabel);
 525
 526                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 527
 528                         if (sabund->getMaxRank() > nseqs) {
 529                                 for(int i = 1; i <=nseqs; i++) {  sabund->set(i, 0); }
 530                         }else { sabund->clear(); }
 531
 532                         if (sabund->getNumBins() > 0) { sabund->print(out); }
 533
 534                         delete sabund;
 535                 }
 536
 537                 return 0;
 538         }
 539         catch(exception& e) {
 540                 m->errorOut(e, "RemoveRareCommand", "processSabund");
 541                 exit(1);
 542         }
 543 }
 544 //**********************************************************************************************************************
 545 int RemoveRareCommand::processRabund(){
 546         try {
 547                 string thisOutputDir = outputDir;
 548                 if (outputDir == "") {  thisOutputDir += m->hasPath(rabundfile);  }
 549                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile);
 550                 outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
 551
 552                 ofstream out;
 553                 m->openOutputFile(outputFileName, out);
 554
 555                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 556                 InputData input(rabundfile, "rabund");
 557                 RAbundVector* rabund = input.getRAbundVector();
 558                 string lastLabel = rabund->getLabel();
 559                 set<string> processedLabels;
 560                 set<string> userLabels = labels;
 561
 562                 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 563
 564                         if (m->control_pressed) { delete rabund; out.close(); return 0; }
 565
 566                         if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 567
 568                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 569                                 processedLabels.insert(rabund->getLabel());
 570                                 userLabels.erase(rabund->getLabel());
 571
 572                                 RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
 573                                 for (int i = 0; i < rabund->getNumBins(); i++) {
 574                                         if (rabund->get(i) > nseqs) {
 575                                                 newRabund.push_back(rabund->get(i));
 576                                         }
 577                                 }
 578                                 if (newRabund.getNumBins() > 0) { newRabund.print(out); }
 579                         }
 580
 581                         if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 582                                 string saveLabel = rabund->getLabel();
 583
 584                                 delete rabund;
 585                                 rabund = input.getRAbundVector(lastLabel);
 586
 587                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 588                                 processedLabels.insert(rabund->getLabel());
 589                                 userLabels.erase(rabund->getLabel());
 590
 591                                 RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
 592                                 for (int i = 0; i < rabund->getNumBins(); i++) {
 593                                         if (rabund->get(i) > nseqs) {
 594                                                 newRabund.push_back(rabund->get(i));
 595                                         }
 596                                 }
 597                                 if (newRabund.getNumBins() > 0) { newRabund.print(out); }
 598
 599                                 //restore real lastlabel to save below
 600                                 rabund->setLabel(saveLabel);
 601                         }
 602
 603                         lastLabel = rabund->getLabel();
 604
 605                         delete rabund;
 606                         rabund = input.getRAbundVector();
 607                 }
 608
 609                 if (m->control_pressed) {  out.close(); return 0; }
 610
 611                 //output error messages about any remaining user labels
 612                 set<string>::iterator it;
 613                 bool needToRun = false;
 614                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 615                         m->mothurOut("Your file does not include the label " + *it);
 616                         if (processedLabels.count(lastLabel) != 1) {
 617                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 618                                 needToRun = true;
 619                         }else {
 620                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 621                         }
 622                 }
 623
 624                 //run last label if you need to
 625                 if (needToRun == true)  {
 626                         if (rabund != NULL) {   delete rabund;  }
 627                         rabund = input.getRAbundVector(lastLabel);
 628
 629                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 630
 631                         RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
 632                         for (int i = 0; i < rabund->getNumBins(); i++) {
 633                                 if (rabund->get(i) > nseqs) {
 634                                         newRabund.push_back(rabund->get(i));
 635                                 }
 636                         }
 637                         if (newRabund.getNumBins() > 0) { newRabund.print(out); }
 638
 639                         delete rabund;
 640                 }
 641
 642                 return 0;
 643         }
 644         catch(exception& e) {
 645                 m->errorOut(e, "RemoveRareCommand", "processRabund");
 646                 exit(1);
 647         }
 648 }
 649 //**********************************************************************************************************************
 650 int RemoveRareCommand::processShared(){
 651         try {
 652                 m->setGroups(Groups);
 653
 654                 string thisOutputDir = outputDir;
 655                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 656                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("shared", sharedfile);
 657                 outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
 658
 659                 ofstream out;
 660                 m->openOutputFile(outputFileName, out);
 661
 662                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 663                 InputData input(sharedfile, "sharedfile");
 664                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 665                 string lastLabel = lookup[0]->getLabel();
 666                 set<string> processedLabels;
 667                 set<string> userLabels = labels;
 668
 669                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 670
 671                         if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  out.close(); return 0; }
 672
 673                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 674
 675                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 676                                 processedLabels.insert(lookup[0]->getLabel());
 677                                 userLabels.erase(lookup[0]->getLabel());
 678
 679                                 if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 680                                 processLookup(lookup, out);
 681                         }
 682
 683                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 684                                 string saveLabel = lookup[0]->getLabel();
 685
 686                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 687                                 lookup = input.getSharedRAbundVectors(lastLabel);
 688
 689                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 690                                 processedLabels.insert(lookup[0]->getLabel());
 691                                 userLabels.erase(lookup[0]->getLabel());
 692
 693                                 if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 694                                 processLookup(lookup, out);
 695
 696                                 //restore real lastlabel to save below
 697                                 lookup[0]->setLabel(saveLabel);
 698                         }
 699
 700                         lastLabel = lookup[0]->getLabel();
 701
 702                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 703                         lookup = input.getSharedRAbundVectors();
 704                 }
 705
 706                 if (m->control_pressed) {  out.close(); return 0; }
 707
 708                 //output error messages about any remaining user labels
 709                 set<string>::iterator it;
 710                 bool needToRun = false;
 711                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 712                         m->mothurOut("Your file does not include the label " + *it);
 713                         if (processedLabels.count(lastLabel) != 1) {
 714                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 715                                 needToRun = true;
 716                         }else {
 717                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 718                         }
 719                 }
 720
 721                 //run last label if you need to
 722                 if (needToRun == true)  {
 723                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       }  }
 724                         lookup = input.getSharedRAbundVectors(lastLabel);
 725
 726                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 727
 728                         if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 729                         processLookup(lookup, out);
 730
 731                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 732                 }
 733
 734                 return 0;
 735         }
 736         catch(exception& e) {
 737                 m->errorOut(e, "RemoveRareCommand", "processSabund");
 738                 exit(1);
 739         }
 740 }
 741 //**********************************************************************************************************************
 742 int RemoveRareCommand::processLookup(vector<SharedRAbundVector*>& lookup, ofstream& out){
 743         try {
 744
 745                 vector<SharedRAbundVector> newRabunds;  newRabunds.resize(lookup.size());
 746                 for (int i = 0; i < lookup.size(); i++) {
 747                         newRabunds[i].setGroup(lookup[i]->getGroup());
 748                         newRabunds[i].setLabel(lookup[i]->getLabel());
 749                 }
 750
 751                 if (byGroup) {
 752
 753                         //for each otu
 754                         for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 755                                 bool allZero = true;
 756
 757                                 if (m->control_pressed) { return 0; }
 758
 759                                 //for each group
 760                                 for (int j = 0; j < lookup.size(); j++) {
 761
 762                                         //are you rare?
 763                                         if (lookup[j]->getAbundance(i) > nseqs) {
 764                                                 newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());
 765                                                 allZero = false;
 766                                         }else {
 767                                                 newRabunds[j].push_back(0, newRabunds[j].getGroup());
 768                                         }
 769                                 }
 770
 771                                 //eliminates zero otus
 772                                 if (allZero) { for (int j = 0; j < newRabunds.size(); j++) {  newRabunds[j].pop_back(); } }
 773                         }
 774                 }else {
 775                         //for each otu
 776                         for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 777
 778                                 if (m->control_pressed) { return 0; }
 779
 780                                 int totalAbund = 0;
 781                                 //get total otu abundance
 782                                 for (int j = 0; j < lookup.size(); j++) {
 783                                         newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());
 784                                         totalAbund += lookup[j]->getAbundance(i);
 785                                 }
 786
 787                                 //eliminates otus below rare cutoff
 788                                 if (totalAbund <= nseqs) { for (int j = 0; j < newRabunds.size(); j++) {  newRabunds[j].pop_back(); } }
 789                         }
 790                 }
 791
 792                 //do we have any otus above the rare cutoff
 793                 if (newRabunds[0].getNumBins() != 0) {
 794                         for (int j = 0; j < newRabunds.size(); j++) {
 795                                 out << newRabunds[j].getLabel() << '\t' << newRabunds[j].getGroup() << '\t';
 796                                 newRabunds[j].print(out);
 797                         }
 798                 }
 799
 800                 return 0;
 801         }
 802         catch(exception& e) {
 803                 m->errorOut(e, "RemoveRareCommand", "processLookup");
 804                 exit(1);
 805         }
 806 }
 807 //**********************************************************************************************************************
 808
 809
 810
 811