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