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", "atleast", "none","list",false,false,true); parameters.push_back(plist);
  20                 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "atleast", "none","rabund",false,false,true); parameters.push_back(prabund);
  21                 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "atleast", "none","sabund",false,false,true); parameters.push_back(psabund);
  22                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "atleast", "none","shared",false,false,true); parameters.push_back(pshared);
  23         CommandParameter pcount("count", "InputTypes", "", "", "CountGroup", "none", "none","count",false,false); parameters.push_back(pcount);
  24                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false); parameters.push_back(pgroup);
  25                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  26                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  27                 CommandParameter pnseqs("nseqs", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnseqs);
  28                 CommandParameter pbygroup("bygroup", "Boolean", "", "f", "", "", "","",false,false); parameters.push_back(pbygroup);
  29                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  30                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  31
  32                 vector<string> myArray;
  33                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "RemoveRareCommand", "setParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 string RemoveRareCommand::getHelpString(){
  43         try {
  44                 string helpString = "";
  45                 helpString += "The remove.rare command parameters are list, rabund, sabund, shared, group, count, label, groups, bygroup and nseqs.\n";
  46                 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";
  47                 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";
  48                 helpString += "The label parameter is used to analyze specific labels in your input. default=all. You may separate label names with dashes.\n";
  49                 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";
  50                 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";
  51                 helpString += "The nseqs parameter allows you to set the cutoff for an otu to be deemed rare. It is required.\n";
  52                 helpString += "The remove.rare command should be in the following format: remove.rare(shared=yourSharedFile, nseqs=yourRareCutoff).\n";
  53                 helpString += "Example remove.rare(shared=amazon.fn.shared, nseqs=2).\n";
  54                 helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedFile).\n";
  55                 return helpString;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "RemoveRareCommand", "getHelpString");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 string RemoveRareCommand::getOutputPattern(string type) {
  64     try {
  65         string pattern = "";
  66
  67         if (type == "rabund")            {   pattern = "[filename],pick,[extension]";    }
  68         else if (type == "sabund")    {   pattern = "[filename],pick,[extension]";    }
  69         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
  70         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
  71         else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
  72         else if (type == "shared")      {   pattern = "[filename],[tag],pick,[extension]";    }
  73         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  74
  75         return pattern;
  76     }
  77     catch(exception& e) {
  78         m->errorOut(e, "RemoveRareCommand", "getOutputPattern");
  79         exit(1);
  80     }
  81 }
  82 //**********************************************************************************************************************
  83 RemoveRareCommand::RemoveRareCommand(){
  84         try {
  85                 abort = true; calledHelp = true;
  86                 setParameters();
  87                 vector<string> tempOutNames;
  88                 outputTypes["rabund"] = tempOutNames;
  89                 outputTypes["sabund"] = tempOutNames;
  90                 outputTypes["list"] = tempOutNames;
  91                 outputTypes["group"] = tempOutNames;
  92         outputTypes["count"] = tempOutNames;
  93                 outputTypes["shared"] = tempOutNames;
  94         }
  95         catch(exception& e) {
  96                 m->errorOut(e, "RemoveRareCommand", "RemoveRareCommand");
  97                 exit(1);
  98         }
  99 }
 100 //**********************************************************************************************************************
 101 RemoveRareCommand::RemoveRareCommand(string option)  {
 102         try {
 103                 abort = false; calledHelp = false;
 104                 allLines = 1;
 105
 106                 //allow user to run help
 107                 if(option == "help") { help(); abort = true; calledHelp = true; }
 108                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 109
 110                 else {
 111                         vector<string> myArray = setParameters();
 112
 113                         OptionParser parser(option);
 114                         map<string,string> parameters = parser.getParameters();
 115
 116                         ValidParameters validParameter;
 117                         map<string,string>::iterator it;
 118
 119                         //check to make sure all parameters are valid for command
 120                         for (it = parameters.begin(); it != parameters.end(); it++) {
 121                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 122                         }
 123
 124                         //initialize outputTypes
 125                         vector<string> tempOutNames;
 126                         outputTypes["rabund"] = tempOutNames;
 127                         outputTypes["sabund"] = tempOutNames;
 128                         outputTypes["list"] = tempOutNames;
 129                         outputTypes["group"] = tempOutNames;
 130                         outputTypes["shared"] = tempOutNames;
 131             outputTypes["count"] = tempOutNames;
 132
 133                         //if the user changes the output directory command factory will send this info to us in the output parameter
 134                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 135
 136                         //if the user changes the input directory command factory will send this info to us in the output parameter
 137                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 138                         if (inputDir == "not found"){   inputDir = "";          }
 139                         else {
 140                                 string path;
 141                                 it = parameters.find("list");
 142                                 //user has given a template file
 143                                 if(it != parameters.end()){
 144                                         path = m->hasPath(it->second);
 145                                         //if the user has not given a path then, add inputdir. else leave path alone.
 146                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 147                                 }
 148
 149                                 it = parameters.find("group");
 150                                 //user has given a template file
 151                                 if(it != parameters.end()){
 152                                         path = m->hasPath(it->second);
 153                                         //if the user has not given a path then, add inputdir. else leave path alone.
 154                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 155                                 }
 156
 157                                 it = parameters.find("sabund");
 158                                 //user has given a template file
 159                                 if(it != parameters.end()){
 160                                         path = m->hasPath(it->second);
 161                                         //if the user has not given a path then, add inputdir. else leave path alone.
 162                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 163                                 }
 164
 165                                 it = parameters.find("rabund");
 166                                 //user has given a template file
 167                                 if(it != parameters.end()){
 168                                         path = m->hasPath(it->second);
 169                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 171                                 }
 172
 173                                 it = parameters.find("shared");
 174                                 //user has given a template file
 175                                 if(it != parameters.end()){
 176                                         path = m->hasPath(it->second);
 177                                         //if the user has not given a path then, add inputdir. else leave path alone.
 178                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 179                                 }
 180
 181                 it = parameters.find("count");
 182                                 //user has given a template file
 183                                 if(it != parameters.end()){
 184                                         path = m->hasPath(it->second);
 185                                         //if the user has not given a path then, add inputdir. else leave path alone.
 186                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 187                                 }
 188                         }
 189
 190
 191                         //check for file parameters
 192                         listfile = validParameter.validFile(parameters, "list", true);
 193                         if (listfile == "not open") { abort = true; }
 194                         else if (listfile == "not found") {  listfile = "";  }
 195                         else { m->setListFile(listfile); }
 196
 197                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 198                         if (sabundfile == "not open") { abort = true; }
 199                         else if (sabundfile == "not found") {  sabundfile = "";  }
 200                         else { m->setSabundFile(sabundfile); }
 201
 202                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 203                         if (rabundfile == "not open") { abort = true; }
 204                         else if (rabundfile == "not found") {  rabundfile = "";  }
 205                         else { m->setRabundFile(rabundfile); }
 206
 207                         groupfile = validParameter.validFile(parameters, "group", true);
 208                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 209                         else if (groupfile == "not found") {  groupfile = "";  }
 210                         else { m->setGroupFile(groupfile); }
 211
 212                         sharedfile = validParameter.validFile(parameters, "shared", true);
 213                         if (sharedfile == "not open") { sharedfile = "";  abort = true; }
 214                         else if (sharedfile == "not found") {  sharedfile = "";  }
 215                         else { m->setSharedFile(sharedfile); }
 216
 217             countfile = validParameter.validFile(parameters, "count", true);
 218                         if (countfile == "not open") { countfile = ""; abort = true; }
 219                         else if (countfile == "not found") { countfile = "";  }
 220                         else { m->setCountTableFile(countfile); }
 221
 222             if ((groupfile != "") && (countfile != "")) {
 223                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 224             }
 225
 226                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 227                                 //is there are current file available for any of these?
 228                                 //give priority to shared, then list, then rabund, then sabund
 229                                 //if there is a current shared file, use it
 230                                 sharedfile = m->getSharedFile();
 231                                 if (sharedfile != "") {  m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 232                                 else {
 233                                         listfile = m->getListFile();
 234                                         if (listfile != "") {  m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 235                                         else {
 236                                                 rabundfile = m->getRabundFile();
 237                                                 if (rabundfile != "") {  m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 238                                                 else {
 239                                                         sabundfile = m->getSabundFile();
 240                                                         if (sabundfile != "") {  m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 241                                                         else {
 242                                                                 m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file."); m->mothurOutEndLine();
 243                                                                 abort = true;
 244                                                         }
 245                                                 }
 246                                         }
 247                                 }
 248                         }
 249
 250                         groups = validParameter.validFile(parameters, "groups", false);
 251                         if (groups == "not found") { groups = "all"; }
 252                         m->splitAtDash(groups, Groups);
 253
 254                         label = validParameter.validFile(parameters, "label", false);
 255                         if (label == "not found") { label = ""; }
 256                         else {
 257                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 258                                 else { allLines = 1;  }
 259                         }
 260
 261                         string temp = validParameter.validFile(parameters, "nseqs", false);
 262                         if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
 263                         else { m->mothurConvert(temp, nseqs); }
 264
 265                         temp = validParameter.validFile(parameters, "bygroup", false);   if (temp == "not found") { temp = "f"; }
 266                         byGroup = m->isTrue(temp);
 267
 268                         if (byGroup && (sharedfile == "")) { m->mothurOut("The byGroup parameter is only valid with a shared file."); m->mothurOutEndLine(); }
 269
 270                         if (((groupfile != "") || (countfile != "")) && (listfile == "")) { m->mothurOut("A group or count file is only valid with a list file."); m->mothurOutEndLine(); groupfile = ""; countfile = ""; }
 271                 }
 272
 273         }
 274         catch(exception& e) {
 275                 m->errorOut(e, "RemoveRareCommand", "RemoveRareCommand");
 276                 exit(1);
 277         }
 278 }
 279 //**********************************************************************************************************************
 280
 281 int RemoveRareCommand::execute(){
 282         try {
 283
 284                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 285
 286                 if (m->control_pressed) { return 0; }
 287
 288                 //read through the correct file and output lines you want to keep
 289                 if (sabundfile != "")           {               processSabund();        }
 290                 if (rabundfile != "")           {               processRabund();        }
 291                 if (listfile != "")                     {               processList();          }
 292                 if (sharedfile != "")           {               processShared();        }
 293
 294                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 295
 296                 if (outputNames.size() != 0) {
 297                         m->mothurOutEndLine();
 298                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 299                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 300                         m->mothurOutEndLine();
 301
 302                         //set rabund file as new current rabundfile
 303                         string current = "";
 304                         itTypes = outputTypes.find("rabund");
 305                         if (itTypes != outputTypes.end()) {
 306                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 307                         }
 308
 309                         itTypes = outputTypes.find("sabund");
 310                         if (itTypes != outputTypes.end()) {
 311                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 312                         }
 313
 314                         itTypes = outputTypes.find("group");
 315                         if (itTypes != outputTypes.end()) {
 316                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 317                         }
 318
 319                         itTypes = outputTypes.find("list");
 320                         if (itTypes != outputTypes.end()) {
 321                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 322                         }
 323
 324                         itTypes = outputTypes.find("shared");
 325                         if (itTypes != outputTypes.end()) {
 326                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 327                         }
 328
 329             itTypes = outputTypes.find("count");
 330                         if (itTypes != outputTypes.end()) {
 331                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 332                         }
 333                 }
 334
 335                 return 0;
 336         }
 337
 338         catch(exception& e) {
 339                 m->errorOut(e, "RemoveRareCommand", "execute");
 340                 exit(1);
 341         }
 342 }
 343
 344 //**********************************************************************************************************************
 345 int RemoveRareCommand::processList(){
 346         try {
 347                 string thisOutputDir = outputDir;
 348                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 349         map<string, string> variables;
 350         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 351         variables["[extension]"] = m->getExtension(listfile);
 352                 string outputFileName = getOutputFileName("list", variables);
 353         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
 354         variables["[extension]"] = m->getExtension(groupfile);
 355                 string outputGroupFileName = getOutputFileName("group", variables);
 356         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
 357         variables["[extension]"] = m->getExtension(countfile);
 358         string outputCountFileName = getOutputFileName("count", variables);
 359
 360                 ofstream out, outGroup;
 361                 m->openOutputFile(outputFileName, out);
 362
 363                 bool wroteSomething = false;
 364
 365                 //you must provide a label because the names in the listfile need to be consistent
 366                 string thisLabel = "";
 367                 if (allLines) { m->mothurOut("For the listfile you must select one label, using first label in your listfile."); m->mothurOutEndLine(); }
 368                 else if (labels.size() > 1) { m->mothurOut("For the listfile you must select one label, using " + (*labels.begin()) + "."); m->mothurOutEndLine(); thisLabel = *labels.begin(); }
 369                 else { thisLabel = *labels.begin(); }
 370
 371                 InputData input(listfile, "list");
 372                 ListVector* list = input.getListVector();
 373
 374                 //get first one or the one we want
 375                 if (thisLabel != "") {
 376                         //use smart distancing
 377                         set<string> userLabels; userLabels.insert(thisLabel);
 378                         set<string> processedLabels;
 379                         string lastLabel = list->getLabel();
 380                         while((list != NULL) && (userLabels.size() != 0)) {
 381                                 if(userLabels.count(list->getLabel()) == 1){
 382                                         processedLabels.insert(list->getLabel());
 383                                         userLabels.erase(list->getLabel());
 384                                         break;
 385                                 }
 386
 387                                 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 388                                         processedLabels.insert(list->getLabel());
 389                                         userLabels.erase(list->getLabel());
 390                                         delete list;
 391                                         list = input.getListVector(lastLabel);
 392                                         break;
 393                                 }
 394                                 lastLabel = list->getLabel();
 395                                 delete list;
 396                                 list = input.getListVector();
 397                         }
 398                         if (userLabels.size() != 0) {
 399                                 m->mothurOut("Your file does not include the label " + thisLabel + ". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 400                                 list = input.getListVector(lastLabel);
 401                         }
 402                 }
 403
 404                 //if groupfile is given then use it
 405                 GroupMap* groupMap;
 406         CountTable ct;
 407                 if (groupfile != "") {
 408                         groupMap = new GroupMap(groupfile); groupMap->readMap();
 409                         SharedUtil util;
 410                         vector<string> namesGroups = groupMap->getNamesOfGroups();
 411                         util.setGroups(Groups, namesGroups);
 412                         m->openOutputFile(outputGroupFileName, outGroup);
 413                 }else if (countfile != "") {
 414             ct.readTable(countfile, true);
 415             if (ct.hasGroupInfo()) {
 416                 vector<string> namesGroups = ct.getNamesOfGroups();
 417                 SharedUtil util;
 418                 util.setGroups(Groups, namesGroups);
 419             }
 420         }
 421
 422
 423                 if (list != NULL) {
 424                         //make a new list vector
 425                         ListVector newList;
 426                         newList.setLabel(list->getLabel());
 427
 428                         //for each bin
 429                         for (int i = 0; i < list->getNumBins(); i++) {
 430                                 if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close();  m->mothurRemove(outputFileName);  return 0; }
 431
 432                                 //parse out names that are in accnos file
 433                                 string binnames = list->get(i);
 434                                 vector<string> names;
 435                                 string saveBinNames = binnames;
 436                                 m->splitAtComma(binnames, names);
 437                 int binsize = names.size();
 438
 439                                 vector<string> newGroupFile;
 440                                 if (groupfile != "") {
 441                                         vector<string> newNames;
 442                                         saveBinNames = "";
 443                                         for(int k = 0; k < names.size(); k++) {
 444                                                 string group = groupMap->getGroup(names[k]);
 445
 446                                                 if (m->inUsersGroups(group, Groups)) {
 447                                                         newGroupFile.push_back(names[k] + "\t" + group);
 448
 449                                                         newNames.push_back(names[k]);
 450                                                         saveBinNames += names[k] + ",";
 451                                                 }
 452                                         }
 453                                         names = newNames; binsize = names.size();
 454                                         saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1);
 455                                 }else if (countfile != "") {
 456                                         saveBinNames = "";
 457                     binsize = 0;
 458                                         for(int k = 0; k < names.size(); k++) {
 459                         if (ct.hasGroupInfo()) {
 460                             vector<string> thisSeqsGroups = ct.getGroups(names[k]);
 461
 462                             int thisSeqsCount = 0;
 463                             for (int n = 0; n < thisSeqsGroups.size(); n++) {
 464                                 if (m->inUsersGroups(thisSeqsGroups[n], Groups)) {
 465                                     thisSeqsCount += ct.getGroupCount(names[k], thisSeqsGroups[n]);
 466                                 }
 467                             }
 468                             binsize += thisSeqsCount;
 469                             //if you don't have any seqs from the groups the user wants, then remove you.
 470                             if (thisSeqsCount == 0) { newGroupFile.push_back(names[k]); }
 471                             else { saveBinNames += names[k] + ","; }
 472                         }else {
 473                             binsize += ct.getNumSeqs(names[k]);
 474                             saveBinNames += names[k] + ",";
 475                         }
 476                                         }
 477                                         saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1);
 478                 }
 479
 480                                 if (binsize > nseqs) { //keep bin
 481                                         newList.push_back(saveBinNames);
 482                                         if (groupfile != "") {  for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; }  }
 483                     else if (countfile != "") { for(int k = 0; k < newGroupFile.size(); k++) {  ct.remove(newGroupFile[k]); } }
 484                                 }else {  if (countfile != "") {  for(int k = 0; k < names.size(); k++) {  ct.remove(names[k]); } }  }
 485                         }
 486
 487                         //print new listvector
 488                         if (newList.getNumBins() != 0) {
 489                                 wroteSomething = true;
 490                                 newList.print(out);
 491                         }
 492                 }
 493
 494                 out.close();
 495                 if (groupfile != "") { outGroup.close(); outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName); }
 496         if (countfile != "") {
 497             if (ct.hasGroupInfo()) {
 498                 vector<string> allGroups = ct.getNamesOfGroups();
 499                 for (int i = 0; i < allGroups.size(); i++) {
 500                     if (!m->inUsersGroups(allGroups[i], Groups)) { ct.removeGroup(allGroups[i]); }
 501                 }
 502
 503             }
 504             ct.printTable(outputCountFileName);
 505             outputTypes["count"].push_back(outputCountFileName); outputNames.push_back(outputCountFileName);
 506         }
 507
 508                 if (wroteSomething == false) {  m->mothurOut("Your file contains only rare sequences."); m->mothurOutEndLine();  }
 509                 outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 510
 511                 return 0;
 512         }
 513         catch(exception& e) {
 514                 m->errorOut(e, "RemoveRareCommand", "processList");
 515                 exit(1);
 516         }
 517 }
 518 //**********************************************************************************************************************
 519 int RemoveRareCommand::processSabund(){
 520         try {
 521                 string thisOutputDir = outputDir;
 522                 if (outputDir == "") {  thisOutputDir += m->hasPath(sabundfile);  }
 523         map<string, string> variables;
 524         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile));
 525         variables["[extension]"] = m->getExtension(sabundfile);
 526                 string outputFileName = getOutputFileName("sabund", variables);
 527                 outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
 528
 529                 ofstream out;
 530                 m->openOutputFile(outputFileName, out);
 531
 532                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 533                 InputData input(sabundfile, "sabund");
 534                 SAbundVector* sabund = input.getSAbundVector();
 535                 string lastLabel = sabund->getLabel();
 536                 set<string> processedLabels;
 537                 set<string> userLabels = labels;
 538
 539                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 540
 541                         if (m->control_pressed) { delete sabund; out.close(); return 0; }
 542
 543                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 544
 545                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 546                                 processedLabels.insert(sabund->getLabel());
 547                                 userLabels.erase(sabund->getLabel());
 548
 549                                 if (sabund->getMaxRank() > nseqs) {
 550                                         for(int i = 1; i <=nseqs; i++) {  sabund->set(i, 0); }
 551                                 }else { sabund->clear(); }
 552
 553                                 if (sabund->getNumBins() > 0) { sabund->print(out); }
 554                         }
 555
 556                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 557                                 string saveLabel = sabund->getLabel();
 558
 559                                 delete sabund;
 560                                 sabund = input.getSAbundVector(lastLabel);
 561
 562                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 563                                 processedLabels.insert(sabund->getLabel());
 564                                 userLabels.erase(sabund->getLabel());
 565
 566                                 if (sabund->getMaxRank() > nseqs) {
 567                                         for(int i = 1; i <=nseqs; i++) {  sabund->set(i, 0); }
 568                                 }else { sabund->clear(); }
 569
 570                                 if (sabund->getNumBins() > 0) { sabund->print(out); }
 571
 572                                 //restore real lastlabel to save below
 573                                 sabund->setLabel(saveLabel);
 574                         }
 575
 576                         lastLabel = sabund->getLabel();
 577
 578                         delete sabund;
 579                         sabund = input.getSAbundVector();
 580                 }
 581
 582                 if (m->control_pressed) {  out.close(); return 0; }
 583
 584                 //output error messages about any remaining user labels
 585                 set<string>::iterator it;
 586                 bool needToRun = false;
 587                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 588                         m->mothurOut("Your file does not include the label " + *it);
 589                         if (processedLabels.count(lastLabel) != 1) {
 590                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 591                                 needToRun = true;
 592                         }else {
 593                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 594                         }
 595                 }
 596
 597                 //run last label if you need to
 598                 if (needToRun == true)  {
 599                         if (sabund != NULL) {   delete sabund;  }
 600                         sabund = input.getSAbundVector(lastLabel);
 601
 602                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 603
 604                         if (sabund->getMaxRank() > nseqs) {
 605                                 for(int i = 1; i <=nseqs; i++) {  sabund->set(i, 0); }
 606                         }else { sabund->clear(); }
 607
 608                         if (sabund->getNumBins() > 0) { sabund->print(out); }
 609
 610                         delete sabund;
 611                 }
 612
 613                 return 0;
 614         }
 615         catch(exception& e) {
 616                 m->errorOut(e, "RemoveRareCommand", "processSabund");
 617                 exit(1);
 618         }
 619 }
 620 //**********************************************************************************************************************
 621 int RemoveRareCommand::processRabund(){
 622         try {
 623                 string thisOutputDir = outputDir;
 624                 if (outputDir == "") {  thisOutputDir += m->hasPath(rabundfile);  }
 625         map<string, string> variables;
 626         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile));
 627         variables["[extension]"] = m->getExtension(rabundfile);
 628                 string outputFileName = getOutputFileName("rabund", variables);
 629                 outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
 630
 631                 ofstream out;
 632                 m->openOutputFile(outputFileName, out);
 633
 634                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 635                 InputData input(rabundfile, "rabund");
 636                 RAbundVector* rabund = input.getRAbundVector();
 637                 string lastLabel = rabund->getLabel();
 638                 set<string> processedLabels;
 639                 set<string> userLabels = labels;
 640
 641                 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 642
 643                         if (m->control_pressed) { delete rabund; out.close(); return 0; }
 644
 645                         if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 646
 647                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 648                                 processedLabels.insert(rabund->getLabel());
 649                                 userLabels.erase(rabund->getLabel());
 650
 651                                 RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
 652                                 for (int i = 0; i < rabund->getNumBins(); i++) {
 653                                         if (rabund->get(i) > nseqs) {
 654                                                 newRabund.push_back(rabund->get(i));
 655                                         }
 656                                 }
 657                                 if (newRabund.getNumBins() > 0) { newRabund.print(out); }
 658                         }
 659
 660                         if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 661                                 string saveLabel = rabund->getLabel();
 662
 663                                 delete rabund;
 664                                 rabund = input.getRAbundVector(lastLabel);
 665
 666                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 667                                 processedLabels.insert(rabund->getLabel());
 668                                 userLabels.erase(rabund->getLabel());
 669
 670                                 RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
 671                                 for (int i = 0; i < rabund->getNumBins(); i++) {
 672                                         if (rabund->get(i) > nseqs) {
 673                                                 newRabund.push_back(rabund->get(i));
 674                                         }
 675                                 }
 676                                 if (newRabund.getNumBins() > 0) { newRabund.print(out); }
 677
 678                                 //restore real lastlabel to save below
 679                                 rabund->setLabel(saveLabel);
 680                         }
 681
 682                         lastLabel = rabund->getLabel();
 683
 684                         delete rabund;
 685                         rabund = input.getRAbundVector();
 686                 }
 687
 688                 if (m->control_pressed) {  out.close(); return 0; }
 689
 690                 //output error messages about any remaining user labels
 691                 set<string>::iterator it;
 692                 bool needToRun = false;
 693                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 694                         m->mothurOut("Your file does not include the label " + *it);
 695                         if (processedLabels.count(lastLabel) != 1) {
 696                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 697                                 needToRun = true;
 698                         }else {
 699                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 700                         }
 701                 }
 702
 703                 //run last label if you need to
 704                 if (needToRun == true)  {
 705                         if (rabund != NULL) {   delete rabund;  }
 706                         rabund = input.getRAbundVector(lastLabel);
 707
 708                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 709
 710                         RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
 711                         for (int i = 0; i < rabund->getNumBins(); i++) {
 712                                 if (rabund->get(i) > nseqs) {
 713                                         newRabund.push_back(rabund->get(i));
 714                                 }
 715                         }
 716                         if (newRabund.getNumBins() > 0) { newRabund.print(out); }
 717
 718                         delete rabund;
 719                 }
 720
 721                 return 0;
 722         }
 723         catch(exception& e) {
 724                 m->errorOut(e, "RemoveRareCommand", "processRabund");
 725                 exit(1);
 726         }
 727 }
 728 //**********************************************************************************************************************
 729 int RemoveRareCommand::processShared(){
 730         try {
 731                 m->setGroups(Groups);
 732
 733                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 734                 InputData input(sharedfile, "sharedfile");
 735                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 736                 string lastLabel = lookup[0]->getLabel();
 737                 set<string> processedLabels;
 738                 set<string> userLabels = labels;
 739
 740                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 741
 742                         if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }   return 0; }
 743
 744                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 745
 746                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 747                                 processedLabels.insert(lookup[0]->getLabel());
 748                                 userLabels.erase(lookup[0]->getLabel());
 749
 750                                 processLookup(lookup);
 751                         }
 752
 753                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 754                                 string saveLabel = lookup[0]->getLabel();
 755
 756                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 757                                 lookup = input.getSharedRAbundVectors(lastLabel);
 758
 759                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 760                                 processedLabels.insert(lookup[0]->getLabel());
 761                                 userLabels.erase(lookup[0]->getLabel());
 762
 763                                 processLookup(lookup);
 764
 765                                 //restore real lastlabel to save below
 766                                 lookup[0]->setLabel(saveLabel);
 767                         }
 768
 769                         lastLabel = lookup[0]->getLabel();
 770
 771                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 772                         lookup = input.getSharedRAbundVectors();
 773                 }
 774
 775                 if (m->control_pressed) {  return 0; }
 776
 777                 //output error messages about any remaining user labels
 778                 set<string>::iterator it;
 779                 bool needToRun = false;
 780                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 781                         m->mothurOut("Your file does not include the label " + *it);
 782                         if (processedLabels.count(lastLabel) != 1) {
 783                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 784                                 needToRun = true;
 785                         }else {
 786                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 787                         }
 788                 }
 789
 790                 //run last label if you need to
 791                 if (needToRun == true)  {
 792                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i];       }  }
 793                         lookup = input.getSharedRAbundVectors(lastLabel);
 794
 795                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 796                         processLookup(lookup);
 797
 798                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 799                 }
 800
 801                 return 0;
 802         }
 803         catch(exception& e) {
 804                 m->errorOut(e, "RemoveRareCommand", "processSabund");
 805                 exit(1);
 806         }
 807 }
 808 //**********************************************************************************************************************
 809 int RemoveRareCommand::processLookup(vector<SharedRAbundVector*>& lookup){
 810         try {
 811
 812         string thisOutputDir = outputDir;
 813                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 814         map<string, string> variables;
 815         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 816         variables["[extension]"] = m->getExtension(sharedfile);
 817         variables["[tag]"] = lookup[0]->getLabel();
 818                 string outputFileName = getOutputFileName("shared", variables);
 819                 outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
 820
 821                 ofstream out;
 822                 m->openOutputFile(outputFileName, out);
 823
 824                 vector<SharedRAbundVector> newRabunds;  newRabunds.resize(lookup.size());
 825         vector<string> headers;
 826                 for (int i = 0; i < lookup.size(); i++) {
 827                         newRabunds[i].setGroup(lookup[i]->getGroup());
 828                         newRabunds[i].setLabel(lookup[i]->getLabel());
 829                 }
 830
 831                 if (byGroup) {
 832
 833                         //for each otu
 834                         for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 835                                 bool allZero = true;
 836
 837                                 if (m->control_pressed) { out.close(); return 0; }
 838
 839                                 //for each group
 840                                 for (int j = 0; j < lookup.size(); j++) {
 841
 842                                         //are you rare?
 843                                         if (lookup[j]->getAbundance(i) > nseqs) {
 844                                                 newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());
 845                                                 allZero = false;
 846                                         }else {
 847                                                 newRabunds[j].push_back(0, newRabunds[j].getGroup());
 848                                         }
 849                                 }
 850
 851                                 //eliminates zero otus
 852                                 if (allZero) { for (int j = 0; j < newRabunds.size(); j++) {  newRabunds[j].pop_back(); } }
 853                 else { headers.push_back(m->currentBinLabels[i]); }
 854                         }
 855                 }else {
 856                         //for each otu
 857                         for (int i = 0; i < lookup[0]->getNumBins(); i++) {
 858
 859                                 if (m->control_pressed) { out.close(); return 0; }
 860
 861                                 int totalAbund = 0;
 862                                 //get total otu abundance
 863                                 for (int j = 0; j < lookup.size(); j++) {
 864                                         newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());
 865                                         totalAbund += lookup[j]->getAbundance(i);
 866                                 }
 867
 868                                 //eliminates otus below rare cutoff
 869                                 if (totalAbund <= nseqs) { for (int j = 0; j < newRabunds.size(); j++) {  newRabunds[j].pop_back(); } }
 870                 else { headers.push_back(m->currentBinLabels[i]); }
 871                         }
 872                 }
 873
 874                 //do we have any otus above the rare cutoff
 875                 if (newRabunds[0].getNumBins() != 0) {
 876             out << "label\tGroup\tnumOtus\t";
 877             for (int j = 0; j < headers.size(); j++) { out << headers[j] << '\t'; }
 878             out << endl;
 879                         for (int j = 0; j < newRabunds.size(); j++) {
 880                                 out << newRabunds[j].getLabel() << '\t' << newRabunds[j].getGroup() << '\t';
 881                                 newRabunds[j].print(out);
 882                         }
 883                 }
 884
 885         out.close();
 886
 887                 return 0;
 888         }
 889         catch(exception& e) {
 890                 m->errorOut(e, "RemoveRareCommand", "processLookup");
 891                 exit(1);
 892         }
 893 }
 894 //**********************************************************************************************************************
 895
 896
 897
 898