subsamplecommand.cpp

   1 /*
   2  *  subsamplecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 10/27/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "subsamplecommand.h"
  11 #include "sharedutilities.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> SubSampleCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta", "group", "list","shared","rabund", "name","sabund","size","groups","label","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "SubSampleCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 SubSampleCommand::SubSampleCommand(){
  27         try {
  28                 abort = true;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["shared"] = tempOutNames;
  32                 outputTypes["list"] = tempOutNames;
  33                 outputTypes["rabund"] = tempOutNames;
  34                 outputTypes["sabund"] = tempOutNames;
  35                 outputTypes["fasta"] = tempOutNames;
  36                 outputTypes["name"] = tempOutNames;
  37                 outputTypes["group"] = tempOutNames;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 vector<string> SubSampleCommand::getRequiredParameters(){
  46         try {
  47                 string Array[] =  {"fasta","list","shared","rabund", "sabund","or"};
  48                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  49                 return myArray;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "SubSampleCommand", "getRequiredParameters");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 vector<string> SubSampleCommand::getRequiredFiles(){
  58         try {
  59                 vector<string> myArray;
  60                 return myArray;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "SubSampleCommand", "getRequiredFiles");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68 SubSampleCommand::SubSampleCommand(string option) {
  69         try {
  70                 globaldata = GlobalData::getInstance();
  71                 abort = false;
  72                 allLines = 1;
  73                 labels.clear();
  74
  75                 //allow user to run help
  76                 if(option == "help") { help(); abort = true; }
  77
  78                 else {
  79                         //valid paramters for this command
  80                         string Array[] =  {"fasta", "group", "list","shared","rabund", "sabund","name","size","groups","label","outputdir","inputdir"};
  81                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  82
  83                         OptionParser parser(option);
  84                         map<string,string> parameters = parser.getParameters();
  85
  86                         ValidParameters validParameter;
  87
  88                         //check to make sure all parameters are valid for command
  89                         map<string,string>::iterator it;
  90                         for (it = parameters.begin(); it != parameters.end(); it++) {
  91                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  92                         }
  93
  94                         //initialize outputTypes
  95                         vector<string> tempOutNames;
  96                         outputTypes["shared"] = tempOutNames;
  97                         outputTypes["list"] = tempOutNames;
  98                         outputTypes["rabund"] = tempOutNames;
  99                         outputTypes["sabund"] = tempOutNames;
 100                         outputTypes["fasta"] = tempOutNames;
 101                         outputTypes["name"] = tempOutNames;
 102                         outputTypes["group"] = tempOutNames;
 103
 104                         //if the user changes the output directory command factory will send this info to us in the output parameter
 105                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 106
 107                         //if the user changes the input directory command factory will send this info to us in the output parameter
 108                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 109                         if (inputDir == "not found"){   inputDir = "";          }
 110                         else {
 111                                 string path;
 112                                 it = parameters.find("list");
 113                                 //user has given a template file
 114                                 if(it != parameters.end()){
 115                                         path = m->hasPath(it->second);
 116                                         //if the user has not given a path then, add inputdir. else leave path alone.
 117                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 118                                 }
 119
 120                                 it = parameters.find("fasta");
 121                                 //user has given a template file
 122                                 if(it != parameters.end()){
 123                                         path = m->hasPath(it->second);
 124                                         //if the user has not given a path then, add inputdir. else leave path alone.
 125                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 126                                 }
 127
 128                                 it = parameters.find("shared");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 134                                 }
 135
 136                                 it = parameters.find("group");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 142                                 }
 143
 144                                 it = parameters.find("sabund");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 150                                 }
 151
 152                                 it = parameters.find("rabund");
 153                                 //user has given a template file
 154                                 if(it != parameters.end()){
 155                                         path = m->hasPath(it->second);
 156                                         //if the user has not given a path then, add inputdir. else leave path alone.
 157                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 158                                 }
 159
 160                                 it = parameters.find("name");
 161                                 //user has given a template file
 162                                 if(it != parameters.end()){
 163                                         path = m->hasPath(it->second);
 164                                         //if the user has not given a path then, add inputdir. else leave path alone.
 165                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 166                                 }
 167                         }
 168
 169                         //check for required parameters
 170                         listfile = validParameter.validFile(parameters, "list", true);
 171                         if (listfile == "not open") { listfile = ""; abort = true; }
 172                         else if (listfile == "not found") { listfile = ""; }
 173
 174                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 175                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 176                         else if (sabundfile == "not found") { sabundfile = ""; }
 177
 178                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 179                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 180                         else if (rabundfile == "not found") { rabundfile = ""; }
 181
 182                         fastafile = validParameter.validFile(parameters, "fasta", true);
 183                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 184                         else if (fastafile == "not found") { fastafile = ""; }
 185
 186                         sharedfile = validParameter.validFile(parameters, "shared", true);
 187                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 188                         else if (sharedfile == "not found") { sharedfile = ""; }
 189
 190                         namefile = validParameter.validFile(parameters, "name", true);
 191                         if (namefile == "not open") { namefile = ""; abort = true; }
 192                         else if (namefile == "not found") { namefile = ""; }
 193
 194                         groupfile = validParameter.validFile(parameters, "group", true);
 195                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 196                         else if (groupfile == "not found") { groupfile = ""; }
 197
 198
 199                         //check for optional parameter and set defaults
 200                         // ...at some point should added some additional type checking...
 201                         label = validParameter.validFile(parameters, "label", false);
 202                         if (label == "not found") { label = ""; }
 203                         else {
 204                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 205                                 else { allLines = 1;  }
 206                         }
 207
 208                         groups = validParameter.validFile(parameters, "groups", false);
 209                         if (groups == "not found") { groups = ""; pickedGroups = false; }
 210                         else {
 211                                 pickedGroups = true;
 212                                 m->splitAtDash(groups, Groups);
 213                                 globaldata->Groups = Groups;
 214                         }
 215
 216                         string temp = validParameter.validFile(parameters, "size", false);              if (temp == "not found"){       temp = "0";             }
 217                         convert(temp, size);
 218
 219                         if ((namefile != "") && (fastafile == "")) { m->mothurOut("You may only use a namefile with a fastafile."); m->mothurOutEndLine(); abort = true; }
 220
 221                         if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) {
 222                                 m->mothurOut("You must provide a fasta, list, sabund, rabund or shared file as an input file."); m->mothurOutEndLine(); abort = true; }
 223
 224                         if (pickedGroups && ((groupfile == "") && (sharedfile == ""))) {
 225                                 m->mothurOut("You cannot pick groups without a valid group file or shared file."); m->mothurOutEndLine(); abort = true; }
 226
 227                         if ((groupfile != "") && ((fastafile == "") && (listfile == ""))) {
 228                                 m->mothurOut("Group file only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
 229
 230                         if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) {
 231                                 m->mothurOut("A new group file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
 232
 233                 }
 234
 235         }
 236         catch(exception& e) {
 237                 m->errorOut(e, "SubSampleCommand", "SubSampleCommand");
 238                 exit(1);
 239         }
 240 }
 241
 242 //**********************************************************************************************************************
 243
 244 void SubSampleCommand::help(){
 245         try {
 246                 m->mothurOut("The sub.sample command is designed to be used as a way to normalize your data, or create a smaller set from your original set.\n");
 247                 m->mothurOut("The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size and label.  You must provide a fasta, list, sabund, rabund or shared file as an input file.\n");
 248                 m->mothurOut("The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n");
 249                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
 250                 m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
 251                 m->mothurOut("The size parameter allows you indicate the size of your subsample.\n");
 252                 m->mothurOut("The size parameter is not set: with shared file size=number of seqs in smallest sample, with all other files, 10% of number of seqs.\n");
 253                 m->mothurOut("The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n");
 254                 m->mothurOut("Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n");
 255                 m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
 256                 m->mothurOut("The sub.sample command outputs a .subsample file.\n");
 257                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 258
 259         }
 260         catch(exception& e) {
 261                 m->errorOut(e, "SubSampleCommand", "help");
 262                 exit(1);
 263         }
 264 }
 265
 266 //**********************************************************************************************************************
 267
 268 SubSampleCommand::~SubSampleCommand(){}
 269
 270 //**********************************************************************************************************************
 271
 272 int SubSampleCommand::execute(){
 273         try {
 274
 275                 if (abort == true) { return 0; }
 276
 277                 if (sharedfile != "")   {   getSubSampleShared();       }
 278                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 279
 280                 if (listfile != "")             {   getSubSampleList();         }
 281                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 282
 283                 if (rabundfile != "")   {   getSubSampleRabund();       }
 284                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 285
 286                 if (sabundfile != "")   {   getSubSampleSabund();       }
 287                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 288
 289                 if (fastafile != "")    {   getSubSampleFasta();        }
 290                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 291
 292
 293                 m->mothurOutEndLine();
 294                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 295                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 296                 m->mothurOutEndLine();
 297
 298                 return 0;
 299         }
 300         catch(exception& e) {
 301                 m->errorOut(e, "SubSampleCommand", "execute");
 302                 exit(1);
 303         }
 304 }
 305 //**********************************************************************************************************************
 306 int SubSampleCommand::getSubSampleFasta() {
 307         try {
 308
 309                 if (namefile != "") { readNames(); }    //fills names with all names in namefile.
 310                 else { getNames(); }//no name file, so get list of names to pick from
 311
 312                 GroupMap* groupMap;
 313                 if (groupfile != "") {
 314
 315                         groupMap = new GroupMap(groupfile);
 316                         groupMap->readMap();
 317
 318                         //takes care of user setting groupNames that are invalid or setting groups=all
 319                         SharedUtil* util = new SharedUtil();
 320                         util->setGroups(Groups, groupMap->namesOfGroups);
 321                         delete util;
 322
 323                         //file mismatch quit
 324                         if (names.size() != groupMap->getNumSeqs()) {
 325                                 m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 326                                 m->mothurOutEndLine();
 327                                 delete groupMap;
 328                                 return 0;
 329                         }
 330                 }
 331
 332                 if (m->control_pressed) { return 0; }
 333
 334                 string thisOutputDir = outputDir;
 335                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 336                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
 337
 338                 ofstream out;
 339                 m->openOutputFile(outputFileName, out);
 340                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 341
 342                 //make sure that if your picked groups size is not too big
 343
 344                 if (pickedGroups) {
 345                         int total = 0;
 346                         for(int i = 0; i < Groups.size(); i++) {
 347                                 total += groupMap->getNumSeqs(Groups[i]);
 348                         }
 349
 350                         if (size == 0) { //user has not set size, set size = 10% samples size
 351                                 size = int (total * 0.10);
 352                         }
 353
 354                         if (total < size) {
 355                                 if (size != 0) {
 356                                         m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
 357                                 }
 358                                 size = int (total * 0.10);
 359                         }
 360
 361                         m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
 362                 }
 363
 364                 if (size == 0) { //user has not set size, set size = 10% samples size
 365                         size = int (names.size() * 0.10);
 366                 }
 367
 368                 int thisSize = names.size();
 369                 if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
 370                         size = thisSize;
 371                 }
 372
 373                 random_shuffle(names.begin(), names.end());
 374
 375                 if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); }
 376
 377                 //randomly select a subset of those names to include in the subsample
 378                 set<string> subset; //dont want repeat sequence names added
 379                 for (int j = 0; j < size; j++) {
 380
 381                         if (m->control_pressed) { return 0; }
 382
 383                         //get random sequence to add, making sure we have not already added it
 384                         bool done = false;
 385                         int myrand;
 386                         while (!done) {
 387                                 myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1));
 388
 389                                 if (subset.count(names[myrand]) == 0)  {
 390
 391                                         if (groupfile != "") { //if there is a groupfile given fill in group info
 392                                                 string group = groupMap->getGroup(names[myrand]);
 393                                                 if (group == "not found") { m->mothurOut("[ERROR]: " + names[myrand] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 394
 395                                                 if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 396                                                         if (m->inUsersGroups(group, Groups)) {
 397                                                                 subset.insert(names[myrand]); break;
 398                                                         }
 399                                                 }else{
 400                                                         subset.insert(names[myrand]); break;
 401                                                 }
 402                                         }else{ //save everyone, group
 403                                                 subset.insert(names[myrand]); break;
 404                                         }
 405                                 }
 406                         }
 407                 }
 408
 409                 //read through fasta file outputting only the names on the subsample list
 410                 ifstream in;
 411                 m->openInputFile(fastafile, in);
 412
 413                 string thisname;
 414                 int count = 0;
 415                 map<string, vector<string> >::iterator itNameMap;
 416
 417                 while(!in.eof()){
 418
 419                         if (m->control_pressed) { in.close(); out.close();  return 0; }
 420
 421                         Sequence currSeq(in);
 422                         thisname = currSeq.getName();
 423
 424                         if (thisname != "") {
 425
 426                                 //does the subset contain a sequence that this sequence represents
 427                                 itNameMap = nameMap.find(thisname);
 428                                 if (itNameMap != nameMap.end()) {
 429                                         vector<string> nameRepresents = itNameMap->second;
 430
 431                                         for (int i = 0; i < nameRepresents.size(); i++){
 432                                                 if (subset.count(nameRepresents[i]) != 0) {
 433                                                         out << ">" << nameRepresents[i] << endl << currSeq.getAligned() << endl;
 434                                                         count++;
 435                                                 }
 436                                         }
 437                                 }else{
 438                                         m->mothurOut("[ERROR]: " + thisname + " is not in your namefile, please correct."); m->mothurOutEndLine();
 439                                 }
 440                         }
 441                         m->gobble(in);
 442                 }
 443                 in.close();
 444                 out.close();
 445
 446                 if (count != subset.size()) {
 447                         m->mothurOut("[ERROR]: The subset selected contained " + toString(subset.size()) + " sequences, but I only found " + toString(count) + " of those in the fastafile."); m->mothurOutEndLine();
 448                 }
 449
 450                 //if a groupfile is provided read through the group file only outputting the names on the subsample list
 451                 if (groupfile != "") {
 452
 453                         string groupOutputDir = outputDir;
 454                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
 455                         string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
 456
 457                         ofstream outGroup;
 458                         m->openOutputFile(groupOutputFileName, outGroup);
 459                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
 460
 461                         ifstream inGroup;
 462                         m->openInputFile(groupfile, inGroup);
 463                         string name, group;
 464
 465                         while(!inGroup.eof()){
 466
 467                                 if (m->control_pressed) { inGroup.close(); outGroup.close(); return 0; }
 468
 469                                 inGroup >> name;        m->gobble(inGroup);                     //read from first column
 470                                 inGroup >> group;                       //read from second column
 471
 472                                 //if this name is in the accnos file
 473                                 if (subset.count(name) != 0) {
 474                                         outGroup << name << '\t' << group << endl;
 475                                         subset.erase(name);
 476                                 }
 477
 478                                 m->gobble(inGroup);
 479                         }
 480                         inGroup.close();
 481                         outGroup.close();
 482
 483                         //sanity check
 484                         if (subset.size() != 0) {
 485                                 m->mothurOut("Your groupfile does not match your fasta file."); m->mothurOutEndLine();
 486                                 for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
 487                                         m->mothurOut("[ERROR]: " + *it + " is missing from your groupfile."); m->mothurOutEndLine();
 488                                 }
 489                         }
 490                 }
 491
 492                 return 0;
 493
 494         }
 495         catch(exception& e) {
 496                 m->errorOut(e, "SubSampleCommand", "getSubSampleFasta");
 497                 exit(1);
 498         }
 499 }
 500 //**********************************************************************************************************************
 501 int SubSampleCommand::getNames() {
 502         try {
 503
 504                 ifstream in;
 505                 m->openInputFile(fastafile, in);
 506
 507                 string thisname;
 508                 while(!in.eof()){
 509
 510                         if (m->control_pressed) { in.close(); return 0; }
 511
 512                         Sequence currSeq(in);
 513                         thisname = currSeq.getName();
 514
 515                         if (thisname != "") {
 516                                 vector<string> temp; temp.push_back(thisname);
 517                                 nameMap[thisname] = temp;
 518                                 names.push_back(thisname);
 519                         }
 520                         m->gobble(in);
 521                 }
 522                 in.close();
 523
 524         }
 525         catch(exception& e) {
 526                 m->errorOut(e, "SubSampleCommand", "getNames");
 527                 exit(1);
 528         }
 529 }
 530 //**********************************************************************************************************************
 531 int SubSampleCommand::readNames() {
 532         try {
 533
 534                 ifstream in;
 535                 m->openInputFile(namefile, in);
 536
 537                 string thisname, repnames;
 538                 map<string, vector<string> >::iterator it;
 539
 540                 while(!in.eof()){
 541
 542                         if (m->control_pressed) { in.close(); return 0; }
 543
 544                         in >> thisname;         m->gobble(in);          //read from first column
 545                         in >> repnames;                 //read from second column
 546
 547                         it = nameMap.find(thisname);
 548                         if (it == nameMap.end()) {
 549
 550                                 vector<string> splitRepNames;
 551                                 m->splitAtComma(repnames, splitRepNames);
 552
 553                                 nameMap[thisname] = splitRepNames;
 554                                 for (int i = 0; i < splitRepNames.size(); i++) { names.push_back(splitRepNames[i]); }
 555
 556                         }else{  m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine();  }
 557
 558                         m->gobble(in);
 559                 }
 560                 in.close();
 561
 562         }
 563         catch(exception& e) {
 564                 m->errorOut(e, "SubSampleCommand", "readNames");
 565                 exit(1);
 566         }
 567 }
 568 //**********************************************************************************************************************
 569 int SubSampleCommand::getSubSampleShared() {
 570         try {
 571
 572                 string thisOutputDir = outputDir;
 573                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 574                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "subsample" + m->getExtension(sharedfile);
 575
 576                 ofstream out;
 577                 m->openOutputFile(outputFileName, out);
 578                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 579
 580                 InputData* input = new InputData(sharedfile, "sharedfile");
 581                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 582                 string lastLabel = lookup[0]->getLabel();
 583
 584                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 585                 set<string> processedLabels;
 586                 set<string> userLabels = labels;
 587
 588                 if (size == 0) { //user has not set size, set size = smallest samples size
 589                         size = lookup[0]->getNumSeqs();
 590                         for (int i = 1; i < lookup.size(); i++) {
 591                                 int thisSize = lookup[i]->getNumSeqs();
 592
 593                                 if (thisSize < size) {  size = thisSize;        }
 594                         }
 595                 }
 596
 597                 m->mothurOut("Sampling " + toString(size) + " from " + toString(lookup[0]->getNumSeqs()) + "."); m->mothurOutEndLine();
 598
 599                 //as long as you are not at the end of the file or done wih the lines you want
 600                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 601                         if (m->control_pressed) {  delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; } out.close(); return 0;  }
 602
 603                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 604
 605                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 606
 607                                 processShared(lookup, out);
 608
 609                                 processedLabels.insert(lookup[0]->getLabel());
 610                                 userLabels.erase(lookup[0]->getLabel());
 611                         }
 612
 613                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 614                                 string saveLabel = lookup[0]->getLabel();
 615
 616                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 617
 618                                 lookup = input->getSharedRAbundVectors(lastLabel);
 619                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 620
 621                                 processShared(lookup, out);
 622
 623                                 processedLabels.insert(lookup[0]->getLabel());
 624                                 userLabels.erase(lookup[0]->getLabel());
 625
 626                                 //restore real lastlabel to save below
 627                                 lookup[0]->setLabel(saveLabel);
 628                         }
 629
 630                         lastLabel = lookup[0]->getLabel();
 631                         //prevent memory leak
 632                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 633
 634                         //get next line to process
 635                         lookup = input->getSharedRAbundVectors();
 636                 }
 637
 638
 639                 if (m->control_pressed) {  out.close(); return 0;  }
 640
 641                 //output error messages about any remaining user labels
 642                 set<string>::iterator it;
 643                 bool needToRun = false;
 644                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 645                         m->mothurOut("Your file does not include the label " + *it);
 646                         if (processedLabels.count(lastLabel) != 1) {
 647                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 648                                 needToRun = true;
 649                         }else {
 650                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 651                         }
 652                 }
 653
 654                 //run last label if you need to
 655                 if (needToRun == true)  {
 656                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 657                         lookup = input->getSharedRAbundVectors(lastLabel);
 658
 659                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 660
 661                         processShared(lookup, out);
 662
 663                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 664                 }
 665
 666                 delete input;
 667                 out.close();
 668
 669                 return 0;
 670
 671         }
 672         catch(exception& e) {
 673                 m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
 674                 exit(1);
 675         }
 676 }
 677 //**********************************************************************************************************************
 678 int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofstream& out) {
 679         try {
 680
 681                 int numBins = thislookup[0]->getNumBins();
 682                 for (int i = 0; i < thislookup.size(); i++) {
 683                         int thisSize = thislookup[i]->getNumSeqs();
 684
 685                         if (thisSize != size) {
 686
 687                                 string thisgroup = thislookup[i]->getGroup();
 688
 689                                 OrderVector* order = new OrderVector();
 690                                 for(int p=0;p<numBins;p++){
 691                                         for(int j=0;j<thislookup[i]->getAbundance(p);j++){
 692                                                 order->push_back(p);
 693                                         }
 694                                 }
 695                                 random_shuffle(order->begin(), order->end());
 696
 697                                 SharedRAbundVector* temp = new SharedRAbundVector(numBins);
 698                                 temp->setLabel(thislookup[i]->getLabel());
 699                                 temp->setGroup(thislookup[i]->getGroup());
 700
 701                                 delete thislookup[i];
 702                                 thislookup[i] = temp;
 703
 704
 705                                 for (int j = 0; j < size; j++) {
 706
 707                                         if (m->control_pressed) { delete order; return 0; }
 708
 709                                         //get random number to sample from order between 0 and thisSize-1.
 710                                         int myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1));
 711
 712                                         int bin = order->get(myrand);
 713
 714                                         int abund = thislookup[i]->getAbundance(bin);
 715                                         thislookup[i]->set(bin, (abund+1), thisgroup);
 716                                 }
 717                                 delete order;
 718                         }
 719                 }
 720
 721                 //subsampling may have created some otus with no sequences in them
 722                 eliminateZeroOTUS(thislookup);
 723
 724                 if (m->control_pressed) { return 0; }
 725
 726                 for (int i = 0; i < thislookup.size(); i++) {
 727                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 728                         thislookup[i]->print(out);
 729                 }
 730
 731                 return 0;
 732
 733         }
 734         catch(exception& e) {
 735                 m->errorOut(e, "SubSampleCommand", "processShared");
 736                 exit(1);
 737         }
 738 }
 739 //**********************************************************************************************************************
 740 int SubSampleCommand::getSubSampleList() {
 741         try {
 742
 743                 string thisOutputDir = outputDir;
 744                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 745                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile);
 746
 747                 ofstream out;
 748                 m->openOutputFile(outputFileName, out);
 749                 outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 750
 751                 InputData* input = new InputData(listfile, "list");
 752                 ListVector* list = input->getListVector();
 753                 string lastLabel = list->getLabel();
 754
 755                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 756                 set<string> processedLabels;
 757                 set<string> userLabels = labels;
 758
 759                 ofstream outGroup;
 760                 GroupMap* groupMap;
 761                 if (groupfile != "") {
 762
 763                         groupMap = new GroupMap(groupfile);
 764                         groupMap->readMap();
 765
 766                         //takes care of user setting groupNames that are invalid or setting groups=all
 767                         SharedUtil* util = new SharedUtil();
 768                         util->setGroups(Groups, groupMap->namesOfGroups);
 769                         delete util;
 770
 771                         //create outputfiles
 772                         string groupOutputDir = outputDir;
 773                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
 774                         string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
 775
 776                         m->openOutputFile(groupOutputFileName, outGroup);
 777                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
 778
 779                         //file mismatch quit
 780                         if (list->getNumSeqs() != groupMap->getNumSeqs()) {
 781                                 m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 782                                 m->mothurOutEndLine();
 783                                 delete groupMap;
 784                                 delete list;
 785                                 delete input;
 786                                 out.close();
 787                                 outGroup.close();
 788                                 return 0;
 789                         }
 790                 }
 791
 792                 //make sure that if your picked groups size is not too big
 793                 if (pickedGroups) {
 794                         int total = 0;
 795                         for(int i = 0; i < Groups.size(); i++) {
 796                                 total += groupMap->getNumSeqs(Groups[i]);
 797                         }
 798
 799                         if (size == 0) { //user has not set size, set size = 10% samples size
 800                                 size = int (total * 0.10);
 801                         }
 802
 803                         if (total < size) {
 804                                 m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
 805                                 size = int (total * 0.10);
 806                         }
 807
 808                         m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
 809                 }else{
 810
 811                         if (size == 0) { //user has not set size, set size = 10% samples size
 812                                 size = int (list->getNumSeqs() * 0.10);
 813                         }
 814
 815                         int thisSize = list->getNumSeqs();
 816                         if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
 817                                 size = thisSize;
 818                         }
 819
 820                         m->mothurOut("Sampling " + toString(size) + " from " + toString(list->getNumSeqs()) + "."); m->mothurOutEndLine();
 821                 }
 822
 823
 824                 for (int i = 0; i < list->getNumBins(); i++) {
 825                         string binnames = list->get(i);
 826
 827                         //parse names
 828                         string individual = "";
 829                         int length = binnames.length();
 830                         for(int j=0;j<length;j++){
 831                                 if(binnames[j] == ','){
 832
 833                                         if (groupfile != "") { //if there is a groupfile given fill in group info
 834                                                 string group = groupMap->getGroup(individual);
 835                                                 if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 836
 837                                                 if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 838                                                         if (m->inUsersGroups(group, Groups)) {
 839                                                                 names.push_back(individual);
 840                                                         }
 841                                                 }else{
 842                                                         names.push_back(individual);
 843                                                 }
 844                                         }else{ //save everyone, group
 845                                                 names.push_back(individual);
 846                                         }
 847                                         individual = "";
 848                                 }
 849                                 else{
 850                                         individual += binnames[j];
 851                                 }
 852                         }
 853                         //save last name
 854                         if (groupfile != "") { //if there is a groupfile given fill in group info
 855                                 string group = groupMap->getGroup(individual);
 856                                 if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 857
 858                                 if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 859                                         if (m->inUsersGroups(group, Groups)) {
 860                                                 names.push_back(individual);
 861                                         }
 862                                 }else{
 863                                         names.push_back(individual);
 864                                 }
 865                         }else{ //save everyone, group
 866                                 names.push_back(individual);
 867                         }
 868                 }
 869
 870                 random_shuffle(names.begin(), names.end());
 871
 872                 //randomly select a subset of those names to include in the subsample
 873                 set<string> subset; //dont want repeat sequence names added
 874                 for (int j = 0; j < size; j++) {
 875
 876                         if (m->control_pressed) { break; }
 877
 878                         //get random sequence to add, making sure we have not already added it
 879                         bool done = false;
 880                         int myrand;
 881                         while (!done) {
 882                                 myrand = (int)((float)(rand()) / (RAND_MAX / (names.size()-1) + 1));
 883
 884                                 if (subset.count(names[myrand]) == 0)  { subset.insert(names[myrand]); break;   }
 885                         }
 886                 }
 887
 888                 if (groupfile != "") {
 889                         //write out new groupfile
 890                         for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
 891                                 string group = groupMap->getGroup(*it);
 892                                 if (group == "not found") { group = "NOTFOUND"; }
 893
 894                                 outGroup << *it << '\t' << group << endl;
 895                         }
 896                         outGroup.close(); delete groupMap;
 897                 }
 898
 899
 900                 //as long as you are not at the end of the file or done wih the lines you want
 901                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 902
 903                         if (m->control_pressed) {  delete list; delete input; out.close();  return 0;  }
 904
 905                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 906
 907                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 908
 909                                 processList(list, out, subset);
 910
 911                                 processedLabels.insert(list->getLabel());
 912                                 userLabels.erase(list->getLabel());
 913                         }
 914
 915                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 916                                 string saveLabel = list->getLabel();
 917
 918                                 delete list;
 919
 920                                 list = input->getListVector(lastLabel);
 921                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 922
 923                                 processList(list, out, subset);
 924
 925                                 processedLabels.insert(list->getLabel());
 926                                 userLabels.erase(list->getLabel());
 927
 928                                 //restore real lastlabel to save below
 929                                 list->setLabel(saveLabel);
 930                         }
 931
 932                         lastLabel = list->getLabel();
 933
 934                         delete list; list = NULL;
 935
 936                         //get next line to process
 937                         list = input->getListVector();
 938                 }
 939
 940
 941                 if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); return 0;  }
 942
 943                 //output error messages about any remaining user labels
 944                 set<string>::iterator it;
 945                 bool needToRun = false;
 946                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 947                         m->mothurOut("Your file does not include the label " + *it);
 948                         if (processedLabels.count(lastLabel) != 1) {
 949                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 950                                 needToRun = true;
 951                         }else {
 952                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 953                         }
 954                 }
 955
 956                 //run last label if you need to
 957                 if (needToRun == true)  {
 958                         if (list != NULL) { delete list; }
 959
 960                         list = input->getListVector(lastLabel);
 961
 962                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 963
 964                         processList(list, out, subset);
 965
 966                         delete list; list = NULL;
 967                 }
 968
 969                 out.close();
 970                 if (list != NULL) { delete list; }
 971                 delete input;
 972
 973                 return 0;
 974
 975         }
 976         catch(exception& e) {
 977                 m->errorOut(e, "SubSampleCommand", "getSubSampleList");
 978                 exit(1);
 979         }
 980 }
 981 //**********************************************************************************************************************
 982 int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>& subset) {
 983         try {
 984
 985                 int numBins = list->getNumBins();
 986
 987                 ListVector* temp = new ListVector();
 988                 temp->setLabel(list->getLabel());
 989
 990                 for (int i = 0; i < numBins; i++) {
 991
 992                         if (m->control_pressed) { break; }
 993
 994                         string binnames = list->get(i);
 995
 996                         //parse names
 997                         string individual = "";
 998                         string newNames = "";
 999                         int length = binnames.length();
1000                         for(int j=0;j<length;j++){
1001                                 if(binnames[j] == ','){
1002                                         if (subset.count(individual) != 0) {  newNames += individual + ",";  }
1003                                         individual = "";
1004                                 }else{
1005                                         individual += binnames[j];
1006                                 }
1007                         }
1008                         if (subset.count(individual) != 0) {  newNames += individual;  }
1009
1010
1011                         //if there are names in this bin add to new list
1012                         if (newNames != "") {
1013                                 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
1014                                 temp->push_back(newNames);
1015                         }
1016                 }
1017
1018                 delete list;
1019                 list = temp;
1020
1021                 if (m->control_pressed) { return 0; }
1022
1023                 list->print(out);
1024
1025                 return 0;
1026
1027         }
1028         catch(exception& e) {
1029                 m->errorOut(e, "SubSampleCommand", "processList");
1030                 exit(1);
1031         }
1032 }
1033 //**********************************************************************************************************************
1034 int SubSampleCommand::getSubSampleRabund() {
1035         try {
1036
1037                 string thisOutputDir = outputDir;
1038                 if (outputDir == "") {  thisOutputDir += m->hasPath(rabundfile);  }
1039                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile);
1040
1041                 ofstream out;
1042                 m->openOutputFile(outputFileName, out);
1043                 outputTypes["rabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1044
1045                 InputData* input = new InputData(rabundfile, "rabund");
1046                 RAbundVector* rabund = input->getRAbundVector();
1047                 string lastLabel = rabund->getLabel();
1048
1049                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1050                 set<string> processedLabels;
1051                 set<string> userLabels = labels;
1052
1053                 if (size == 0) { //user has not set size, set size = 10%
1054                         size = int((rabund->getNumSeqs()) * 0.10);
1055                 }
1056
1057                 m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1058
1059                 //as long as you are not at the end of the file or done wih the lines you want
1060                 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1061                         if (m->control_pressed) {  delete input; delete rabund; out.close(); return 0;  }
1062
1063                         if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
1064
1065                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1066
1067                                 processRabund(rabund, out);
1068
1069                                 processedLabels.insert(rabund->getLabel());
1070                                 userLabels.erase(rabund->getLabel());
1071                         }
1072
1073                         if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1074                                 string saveLabel = rabund->getLabel();
1075
1076                                 delete rabund;
1077
1078                                 rabund = input->getRAbundVector(lastLabel);
1079                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1080
1081                                 processRabund(rabund, out);
1082
1083                                 processedLabels.insert(rabund->getLabel());
1084                                 userLabels.erase(rabund->getLabel());
1085
1086                                 //restore real lastlabel to save below
1087                                 rabund->setLabel(saveLabel);
1088                         }
1089
1090                         lastLabel = rabund->getLabel();
1091
1092                         //prevent memory leak
1093                         delete rabund; rabund = NULL;
1094
1095                         //get next line to process
1096                         rabund = input->getRAbundVector();
1097                 }
1098
1099
1100                 if (m->control_pressed) {  out.close(); return 0;  }
1101
1102                 //output error messages about any remaining user labels
1103                 set<string>::iterator it;
1104                 bool needToRun = false;
1105                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1106                         m->mothurOut("Your file does not include the label " + *it);
1107                         if (processedLabels.count(lastLabel) != 1) {
1108                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1109                                 needToRun = true;
1110                         }else {
1111                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1112                         }
1113                 }
1114
1115                 //run last label if you need to
1116                 if (needToRun == true)  {
1117                         if (rabund != NULL) { delete rabund; }
1118
1119                         rabund = input->getRAbundVector(lastLabel);
1120
1121                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1122
1123                         processRabund(rabund, out);
1124
1125                         delete rabund;
1126                 }
1127
1128                 delete input;
1129                 out.close();
1130
1131                 return 0;
1132
1133         }
1134         catch(exception& e) {
1135                 m->errorOut(e, "SubSampleCommand", "getSubSampleRabund");
1136                 exit(1);
1137         }
1138 }
1139 //**********************************************************************************************************************
1140 int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) {
1141         try {
1142
1143                 int numBins = rabund->getNumBins();
1144                 int thisSize = rabund->getNumSeqs();
1145
1146                 if (thisSize != size) {
1147
1148                         OrderVector* order = new OrderVector();
1149                         for(int p=0;p<numBins;p++){
1150                                 for(int j=0;j<rabund->get(p);j++){
1151                                         order->push_back(p);
1152                                 }
1153                         }
1154                         random_shuffle(order->begin(), order->end());
1155
1156                         RAbundVector* temp = new RAbundVector(numBins);
1157                         temp->setLabel(rabund->getLabel());
1158
1159                         delete rabund;
1160                         rabund = temp;
1161
1162                         for (int j = 0; j < size; j++) {
1163
1164                                 if (m->control_pressed) { delete order; return 0; }
1165
1166                                 //get random number to sample from order between 0 and thisSize-1.
1167                                 int myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1));
1168
1169                                 int bin = order->get(myrand);
1170
1171                                 int abund = rabund->get(bin);
1172                                 rabund->set(bin, (abund+1));
1173                         }
1174
1175                         delete order;
1176                 }
1177
1178                 if (m->control_pressed) { return 0; }
1179
1180                 rabund->print(out);
1181
1182                 return 0;
1183
1184         }
1185         catch(exception& e) {
1186                 m->errorOut(e, "SubSampleCommand", "processRabund");
1187                 exit(1);
1188         }
1189 }
1190 //**********************************************************************************************************************
1191 int SubSampleCommand::getSubSampleSabund() {
1192         try {
1193
1194                 string thisOutputDir = outputDir;
1195                 if (outputDir == "") {  thisOutputDir += m->hasPath(sabundfile);  }
1196                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile);
1197
1198                 ofstream out;
1199                 m->openOutputFile(outputFileName, out);
1200                 outputTypes["sabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1201
1202                 InputData* input = new InputData(sabundfile, "sabund");
1203                 SAbundVector* sabund = input->getSAbundVector();
1204                 string lastLabel = sabund->getLabel();
1205
1206                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1207                 set<string> processedLabels;
1208                 set<string> userLabels = labels;
1209
1210                 if (size == 0) { //user has not set size, set size = 10%
1211                         size = int((sabund->getNumSeqs()) * 0.10);
1212                 }
1213
1214                 m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1215
1216                 //as long as you are not at the end of the file or done wih the lines you want
1217                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1218                         if (m->control_pressed) {  delete input; delete sabund; out.close(); return 0;  }
1219
1220                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
1221
1222                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1223
1224                                 processSabund(sabund, out);
1225
1226                                 processedLabels.insert(sabund->getLabel());
1227                                 userLabels.erase(sabund->getLabel());
1228                         }
1229
1230                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1231                                 string saveLabel = sabund->getLabel();
1232
1233                                 delete sabund;
1234
1235                                 sabund = input->getSAbundVector(lastLabel);
1236                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1237
1238                                 processSabund(sabund, out);
1239
1240                                 processedLabels.insert(sabund->getLabel());
1241                                 userLabels.erase(sabund->getLabel());
1242
1243                                 //restore real lastlabel to save below
1244                                 sabund->setLabel(saveLabel);
1245                         }
1246
1247                         lastLabel = sabund->getLabel();
1248
1249                         //prevent memory leak
1250                         delete sabund; sabund = NULL;
1251
1252                         //get next line to process
1253                         sabund = input->getSAbundVector();
1254                 }
1255
1256
1257                 if (m->control_pressed) {  out.close(); return 0;  }
1258
1259                 //output error messages about any remaining user labels
1260                 set<string>::iterator it;
1261                 bool needToRun = false;
1262                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1263                         m->mothurOut("Your file does not include the label " + *it);
1264                         if (processedLabels.count(lastLabel) != 1) {
1265                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1266                                 needToRun = true;
1267                         }else {
1268                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1269                         }
1270                 }
1271
1272                 //run last label if you need to
1273                 if (needToRun == true)  {
1274                         if (sabund != NULL) { delete sabund; }
1275
1276                         sabund = input->getSAbundVector(lastLabel);
1277
1278                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1279
1280                         processSabund(sabund, out);
1281
1282                         delete sabund;
1283                 }
1284
1285                 delete input;
1286                 out.close();
1287
1288                 return 0;
1289
1290         }
1291         catch(exception& e) {
1292                 m->errorOut(e, "SubSampleCommand", "getSubSampleSabund");
1293                 exit(1);
1294         }
1295 }
1296 //**********************************************************************************************************************
1297 int SubSampleCommand::processSabund(SAbundVector*& sabund, ofstream& out) {
1298         try {
1299
1300                 RAbundVector* rabund = new RAbundVector();
1301                 *rabund = sabund->getRAbundVector();
1302
1303                 int numBins = rabund->getNumBins();
1304                 int thisSize = rabund->getNumSeqs();
1305
1306                 if (thisSize != size) {
1307
1308                         OrderVector* order = new OrderVector();
1309                         for(int p=0;p<numBins;p++){
1310                                 for(int j=0;j<rabund->get(p);j++){
1311                                         order->push_back(p);
1312                                 }
1313                         }
1314                         random_shuffle(order->begin(), order->end());
1315
1316                         RAbundVector* temp = new RAbundVector(numBins);
1317                         temp->setLabel(rabund->getLabel());
1318
1319                         delete rabund;
1320                         rabund = temp;
1321
1322                         for (int j = 0; j < size; j++) {
1323
1324                                 if (m->control_pressed) { delete order; return 0; }
1325
1326                                 //get random number to sample from order between 0 and thisSize-1.
1327                                 int myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1));
1328
1329                                 int bin = order->get(myrand);
1330
1331                                 int abund = rabund->get(bin);
1332                                 rabund->set(bin, (abund+1));
1333                         }
1334
1335                         delete order;
1336                 }
1337
1338                 if (m->control_pressed) { return 0; }
1339
1340                 delete sabund;
1341                 sabund = new SAbundVector();
1342                 *sabund = rabund->getSAbundVector();
1343                 delete rabund;
1344
1345                 sabund->print(out);
1346
1347                 return 0;
1348
1349         }
1350         catch(exception& e) {
1351                 m->errorOut(e, "SubSampleCommand", "processSabund");
1352                 exit(1);
1353         }
1354 }
1355 //**********************************************************************************************************************
1356 int SubSampleCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
1357         try {
1358
1359                 vector<SharedRAbundVector*> newLookup;
1360                 for (int i = 0; i < thislookup.size(); i++) {
1361                         SharedRAbundVector* temp = new SharedRAbundVector();
1362                         temp->setLabel(thislookup[i]->getLabel());
1363                         temp->setGroup(thislookup[i]->getGroup());
1364                         newLookup.push_back(temp);
1365                 }
1366
1367                 //for each bin
1368                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
1369                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
1370
1371                         //look at each sharedRabund and make sure they are not all zero
1372                         bool allZero = true;
1373                         for (int j = 0; j < thislookup.size(); j++) {
1374                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
1375                         }
1376
1377                         //if they are not all zero add this bin
1378                         if (!allZero) {
1379                                 for (int j = 0; j < thislookup.size(); j++) {
1380                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
1381                                 }
1382                         }
1383                 }
1384
1385                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
1386                 thislookup.clear();
1387
1388                 thislookup = newLookup;
1389
1390                 return 0;
1391
1392         }
1393         catch(exception& e) {
1394                 m->errorOut(e, "SubSampleCommand", "eliminateZeroOTUS");
1395                 exit(1);
1396         }
1397 }
1398
1399 //**********************************************************************************************************************
1400
1401
1402