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 #include "deconvolutecommand.h"
  13 #include "subsample.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> SubSampleCommand::setParameters(){
  17         try {
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pfasta);
  19                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  21                 CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(plist);
  22                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pshared);
  23                 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(prabund);
  24                 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(psabund);
  25                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  26                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  27                 CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
  28                 CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
  29                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  30                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  31
  32                 vector<string> myArray;
  33                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "SubSampleCommand", "setParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 string SubSampleCommand::getHelpString(){
  43         try {
  44                 string helpString = "";
  45                 helpString += "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";
  46                 helpString += "The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size, persample and label.  You must provide a fasta, list, sabund, rabund or shared file as an input file.\n";
  47                 helpString += "The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n";
  48                 helpString += "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";
  49                 helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
  50                 helpString += "The size parameter allows you indicate the size of your subsample.\n";
  51                 helpString += "The persample parameter allows you indicate you want to select subsample of the same size from each of your groups, default=false. It is only used with the list and fasta files if a groupfile is given.\n";
  52                 helpString += "persample=false will select a random set of sequences of the size you select, but the number of seqs from each group may differ.\n";
  53                 helpString += "The size parameter is not set: with shared file size=number of seqs in smallest sample, with all other files if a groupfile is given and persample=true, then size=number of seqs in smallest sample, otherwise size=10% of number of seqs.\n";
  54                 helpString += "The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n";
  55                 helpString += "Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n";
  56                 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
  57                 helpString += "The sub.sample command outputs a .subsample file.\n";
  58                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  59                 return helpString;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "SubSampleCommand", "getHelpString");
  63                 exit(1);
  64         }
  65 }
  66 //**********************************************************************************************************************
  67 SubSampleCommand::SubSampleCommand(){
  68         try {
  69                 abort = true; calledHelp = true;
  70                 setParameters();
  71                 vector<string> tempOutNames;
  72                 outputTypes["shared"] = tempOutNames;
  73                 outputTypes["list"] = tempOutNames;
  74                 outputTypes["rabund"] = tempOutNames;
  75                 outputTypes["sabund"] = tempOutNames;
  76                 outputTypes["fasta"] = tempOutNames;
  77                 outputTypes["name"] = tempOutNames;
  78                 outputTypes["group"] = tempOutNames;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
  82                 exit(1);
  83         }
  84 }
  85 //**********************************************************************************************************************
  86 SubSampleCommand::SubSampleCommand(string option) {
  87         try {
  88                 abort = false; calledHelp = false;
  89                 allLines = 1;
  90
  91                 //allow user to run help
  92                 if(option == "help") { help(); abort = true; calledHelp = true; }
  93                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  94
  95                 else {
  96                         vector<string> myArray = setParameters();
  97
  98                         OptionParser parser(option);
  99                         map<string,string> parameters = parser.getParameters();
 100
 101                         ValidParameters validParameter;
 102
 103                         //check to make sure all parameters are valid for command
 104                         map<string,string>::iterator it;
 105                         for (it = parameters.begin(); it != parameters.end(); it++) {
 106                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 107                         }
 108
 109                         //initialize outputTypes
 110                         vector<string> tempOutNames;
 111                         outputTypes["shared"] = tempOutNames;
 112                         outputTypes["list"] = tempOutNames;
 113                         outputTypes["rabund"] = tempOutNames;
 114                         outputTypes["sabund"] = tempOutNames;
 115                         outputTypes["fasta"] = tempOutNames;
 116                         outputTypes["name"] = tempOutNames;
 117                         outputTypes["group"] = tempOutNames;
 118
 119                         //if the user changes the output directory command factory will send this info to us in the output parameter
 120                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 121
 122                         //if the user changes the input directory command factory will send this info to us in the output parameter
 123                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 124                         if (inputDir == "not found"){   inputDir = "";          }
 125                         else {
 126                                 string path;
 127                                 it = parameters.find("list");
 128                                 //user has given a template file
 129                                 if(it != parameters.end()){
 130                                         path = m->hasPath(it->second);
 131                                         //if the user has not given a path then, add inputdir. else leave path alone.
 132                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 133                                 }
 134
 135                                 it = parameters.find("fasta");
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 141                                 }
 142
 143                                 it = parameters.find("shared");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 149                                 }
 150
 151                                 it = parameters.find("group");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 157                                 }
 158
 159                                 it = parameters.find("sabund");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 165                                 }
 166
 167                                 it = parameters.find("rabund");
 168                                 //user has given a template file
 169                                 if(it != parameters.end()){
 170                                         path = m->hasPath(it->second);
 171                                         //if the user has not given a path then, add inputdir. else leave path alone.
 172                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 173                                 }
 174
 175                                 it = parameters.find("name");
 176                                 //user has given a template file
 177                                 if(it != parameters.end()){
 178                                         path = m->hasPath(it->second);
 179                                         //if the user has not given a path then, add inputdir. else leave path alone.
 180                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 181                                 }
 182                         }
 183
 184                         //check for required parameters
 185                         listfile = validParameter.validFile(parameters, "list", true);
 186                         if (listfile == "not open") { listfile = ""; abort = true; }
 187                         else if (listfile == "not found") { listfile = ""; }
 188                         else { m->setListFile(listfile); }
 189
 190                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 191                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 192                         else if (sabundfile == "not found") { sabundfile = ""; }
 193                         else { m->setSabundFile(sabundfile); }
 194
 195                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 196                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 197                         else if (rabundfile == "not found") { rabundfile = ""; }
 198                         else { m->setRabundFile(rabundfile); }
 199
 200                         fastafile = validParameter.validFile(parameters, "fasta", true);
 201                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 202                         else if (fastafile == "not found") { fastafile = ""; }
 203                         else { m->setFastaFile(fastafile); }
 204
 205                         sharedfile = validParameter.validFile(parameters, "shared", true);
 206                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 207                         else if (sharedfile == "not found") { sharedfile = ""; }
 208                         else { m->setSharedFile(sharedfile); }
 209
 210                         namefile = validParameter.validFile(parameters, "name", true);
 211                         if (namefile == "not open") { namefile = ""; abort = true; }
 212                         else if (namefile == "not found") { namefile = ""; }
 213                         else { m->setNameFile(namefile); }
 214
 215                         groupfile = validParameter.validFile(parameters, "group", true);
 216                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 217                         else if (groupfile == "not found") { groupfile = ""; }
 218                         else { m->setGroupFile(groupfile); }
 219
 220                         //check for optional parameter and set defaults
 221                         // ...at some point should added some additional type checking...
 222                         label = validParameter.validFile(parameters, "label", false);
 223                         if (label == "not found") { label = ""; }
 224                         else {
 225                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 226                                 else { allLines = 1;  }
 227                         }
 228
 229                         groups = validParameter.validFile(parameters, "groups", false);
 230                         if (groups == "not found") { groups = ""; pickedGroups = false; }
 231                         else {
 232                                 pickedGroups = true;
 233                                 m->splitAtDash(groups, Groups);
 234                                 m->setGroups(Groups);
 235                         }
 236
 237                         string temp = validParameter.validFile(parameters, "size", false);              if (temp == "not found"){       temp = "0";             }
 238                         m->mothurConvert(temp, size);
 239
 240                         temp = validParameter.validFile(parameters, "persample", false);                if (temp == "not found"){       temp = "f";             }
 241                         persample = m->isTrue(temp);
 242
 243                         if (groupfile == "") { persample = false; }
 244
 245                         if ((namefile != "") && (fastafile == "")) { m->mothurOut("You may only use a namefile with a fastafile."); m->mothurOutEndLine(); abort = true; }
 246
 247                         if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) {
 248                                 m->mothurOut("You must provide a fasta, list, sabund, rabund or shared file as an input file."); m->mothurOutEndLine(); abort = true; }
 249
 250                         if (pickedGroups && ((groupfile == "") && (sharedfile == ""))) {
 251                                 m->mothurOut("You cannot pick groups without a valid group file or shared file."); m->mothurOutEndLine(); abort = true; }
 252
 253                         if ((groupfile != "") && ((fastafile == "") && (listfile == ""))) {
 254                                 m->mothurOut("Group file only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
 255
 256                         if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) {
 257                                 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; }
 258
 259                         if ((fastafile != "") && (namefile == "")) {
 260                                 vector<string> files; files.push_back(fastafile);
 261                                 parser.getNameFile(files);
 262                         }
 263                 }
 264
 265         }
 266         catch(exception& e) {
 267                 m->errorOut(e, "SubSampleCommand", "SubSampleCommand");
 268                 exit(1);
 269         }
 270 }
 271 //**********************************************************************************************************************
 272
 273 int SubSampleCommand::execute(){
 274         try {
 275
 276                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 277
 278                 if (sharedfile != "")   {   getSubSampleShared();       }
 279                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 280
 281                 if (listfile != "")             {   getSubSampleList();         }
 282                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 283
 284                 if (rabundfile != "")   {   getSubSampleRabund();       }
 285                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 286
 287                 if (sabundfile != "")   {   getSubSampleSabund();       }
 288                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 289
 290                 if (fastafile != "")    {   getSubSampleFasta();        }
 291                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 292
 293                 //set fasta file as new current fastafile
 294                 string current = "";
 295                 itTypes = outputTypes.find("fasta");
 296                 if (itTypes != outputTypes.end()) {
 297                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 298                 }
 299
 300                 itTypes = outputTypes.find("name");
 301                 if (itTypes != outputTypes.end()) {
 302                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 303                 }
 304
 305                 itTypes = outputTypes.find("group");
 306                 if (itTypes != outputTypes.end()) {
 307                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 308                 }
 309
 310                 itTypes = outputTypes.find("list");
 311                 if (itTypes != outputTypes.end()) {
 312                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 313                 }
 314
 315                 itTypes = outputTypes.find("shared");
 316                 if (itTypes != outputTypes.end()) {
 317                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 318                 }
 319
 320                 itTypes = outputTypes.find("rabund");
 321                 if (itTypes != outputTypes.end()) {
 322                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 323                 }
 324
 325                 itTypes = outputTypes.find("sabund");
 326                 if (itTypes != outputTypes.end()) {
 327                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 328                 }
 329
 330
 331                 m->mothurOutEndLine();
 332                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 333                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 334                 m->mothurOutEndLine();
 335
 336                 return 0;
 337         }
 338         catch(exception& e) {
 339                 m->errorOut(e, "SubSampleCommand", "execute");
 340                 exit(1);
 341         }
 342 }
 343 //**********************************************************************************************************************
 344 int SubSampleCommand::getSubSampleFasta() {
 345         try {
 346
 347                 if (namefile != "") { readNames(); }    //fills names with all names in namefile.
 348                 else { getNames(); }//no name file, so get list of names to pick from
 349
 350                 GroupMap* groupMap;
 351                 if (groupfile != "") {
 352
 353                         groupMap = new GroupMap(groupfile);
 354                         groupMap->readMap();
 355
 356                         //takes care of user setting groupNames that are invalid or setting groups=all
 357                         SharedUtil* util = new SharedUtil();
 358                         vector<string> namesGroups = groupMap->getNamesOfGroups();
 359                         util->setGroups(Groups, namesGroups);
 360                         delete util;
 361
 362                         //file mismatch quit
 363                         if (names.size() != groupMap->getNumSeqs()) {
 364                                 m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 365                                 m->mothurOutEndLine();
 366                                 delete groupMap;
 367                                 return 0;
 368                         }
 369                 }
 370
 371                 if (m->control_pressed) { return 0; }
 372
 373
 374                 //make sure that if your picked groups size is not too big
 375                 int thisSize = names.size();
 376                 if (persample) {
 377                         if (size == 0) { //user has not set size, set size = smallest samples size
 378                                 size = groupMap->getNumSeqs(Groups[0]);
 379                                 for (int i = 1; i < Groups.size(); i++) {
 380                                         int thisSize = groupMap->getNumSeqs(Groups[i]);
 381
 382                                         if (thisSize < size) {  size = thisSize;        }
 383                                 }
 384                         }else { //make sure size is not too large
 385                                 vector<string> newGroups;
 386                                 for (int i = 0; i < Groups.size(); i++) {
 387                                         int thisSize = groupMap->getNumSeqs(Groups[i]);
 388
 389                                         if (thisSize >= size) { newGroups.push_back(Groups[i]); }
 390                                         else {  m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
 391                                 }
 392                                 Groups = newGroups;
 393                         }
 394
 395                         m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
 396                 }else {
 397                         if (pickedGroups) {
 398                                 int total = 0;
 399                                 for(int i = 0; i < Groups.size(); i++) {
 400                                         total += groupMap->getNumSeqs(Groups[i]);
 401                                 }
 402
 403                                 if (size == 0) { //user has not set size, set size = 10% samples size
 404                                         size = int (total * 0.10);
 405                                 }
 406
 407                                 if (total < size) {
 408                                         if (size != 0) {
 409                                                 m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
 410                                         }
 411                                         size = int (total * 0.10);
 412                                 }
 413
 414                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
 415                         }
 416
 417                         if (size == 0) { //user has not set size, set size = 10% samples size
 418                                 size = int (names.size() * 0.10);
 419                         }
 420
 421                         if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
 422                                 size = thisSize;
 423                         }
 424
 425                         if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); }
 426
 427                 }
 428                 random_shuffle(names.begin(), names.end());
 429
 430                 set<string> subset; //dont want repeat sequence names added
 431                 if (persample) {
 432                         //initialize counts
 433                         map<string, int> groupCounts;
 434                         map<string, int>::iterator itGroupCounts;
 435                         for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
 436
 437                         for (int j = 0; j < names.size(); j++) {
 438
 439                                 if (m->control_pressed) { return 0; }
 440
 441                                 string group = groupMap->getGroup(names[j]);
 442                                 if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 443                                 else{
 444                                         itGroupCounts = groupCounts.find(group);
 445                                         if (itGroupCounts != groupCounts.end()) {
 446                                                 if (groupCounts[group] < size) {        subset.insert(names[j]);        groupCounts[group]++; }
 447                                         }
 448                                 }
 449                         }
 450                 }else {
 451
 452                         //randomly select a subset of those names to include in the subsample
 453                         //since names was randomly shuffled just grab the next one
 454                         for (int j = 0; j < names.size(); j++) {
 455
 456                                 if (m->control_pressed) { return 0; }
 457
 458                                 if (groupfile != "") { //if there is a groupfile given fill in group info
 459                                         string group = groupMap->getGroup(names[j]);
 460                                         if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 461
 462                                         if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 463                                                 if (m->inUsersGroups(group, Groups)) {
 464                                                         subset.insert(names[j]);
 465                                                 }
 466                                         }else{
 467                                                 subset.insert(names[j]);
 468                                         }
 469                                 }else{ //save everyone, group
 470                                         subset.insert(names[j]);
 471                                 }
 472
 473                                 //do we have enough??
 474                                 if (subset.size() == size) { break; }
 475                         }
 476                 }
 477
 478                 if (subset.size() == 0) {  m->mothurOut("The size you selected is too large, skipping fasta file."); m->mothurOutEndLine();  return 0; }
 479
 480                 string thisOutputDir = outputDir;
 481                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 482                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
 483
 484                 ofstream out;
 485                 m->openOutputFile(outputFileName, out);
 486
 487                 //read through fasta file outputting only the names on the subsample list
 488                 ifstream in;
 489                 m->openInputFile(fastafile, in);
 490
 491                 string thisname;
 492                 int count = 0;
 493                 map<string, vector<string> >::iterator itNameMap;
 494
 495                 while(!in.eof()){
 496
 497                         if (m->control_pressed) { in.close(); out.close();  return 0; }
 498
 499                         Sequence currSeq(in);
 500                         thisname = currSeq.getName();
 501
 502                         if (thisname != "") {
 503
 504                                 //does the subset contain a sequence that this sequence represents
 505                                 itNameMap = nameMap.find(thisname);
 506                                 if (itNameMap != nameMap.end()) {
 507                                         vector<string> nameRepresents = itNameMap->second;
 508
 509                                         for (int i = 0; i < nameRepresents.size(); i++){
 510                                                 if (subset.count(nameRepresents[i]) != 0) {
 511                                                         out << ">" << nameRepresents[i] << endl << currSeq.getAligned() << endl;
 512                                                         count++;
 513                                                 }
 514                                         }
 515                                 }else{
 516                                         m->mothurOut("[ERROR]: " + thisname + " is not in your namefile, please correct."); m->mothurOutEndLine();
 517                                 }
 518                         }
 519                         m->gobble(in);
 520                 }
 521                 in.close();
 522                 out.close();
 523
 524                 if (count != subset.size()) {
 525                         m->mothurOut("[ERROR]: The subset selected contained " + toString(subset.size()) + " sequences, but I only found " + toString(count) + " of those in the fastafile."); m->mothurOutEndLine();
 526                 }
 527
 528                 if (namefile != "") {
 529                         m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
 530
 531                         //use unique.seqs to create new name and fastafile
 532                         string inputString = "fasta=" + outputFileName;
 533                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 534                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 535                         m->mothurCalling = true;
 536
 537                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 538                         uniqueCommand->execute();
 539
 540                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 541
 542                         delete uniqueCommand;
 543                         m->mothurCalling = false;
 544
 545                         outputTypes["name"].push_back(filenames["name"][0]);  outputNames.push_back(filenames["name"][0]);
 546                         m->mothurRemove(outputFileName);
 547                         outputFileName = filenames["fasta"][0];
 548
 549                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 550
 551                         m->mothurOut("Done."); m->mothurOutEndLine();
 552                 }
 553
 554                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 555
 556                 //if a groupfile is provided read through the group file only outputting the names on the subsample list
 557                 if (groupfile != "") {
 558
 559                         string groupOutputDir = outputDir;
 560                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
 561                         string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
 562
 563                         ofstream outGroup;
 564                         m->openOutputFile(groupOutputFileName, outGroup);
 565                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
 566
 567                         ifstream inGroup;
 568                         m->openInputFile(groupfile, inGroup);
 569                         string name, group;
 570
 571                         while(!inGroup.eof()){
 572
 573                                 if (m->control_pressed) { inGroup.close(); outGroup.close(); return 0; }
 574
 575                                 inGroup >> name;        m->gobble(inGroup);                     //read from first column
 576                                 inGroup >> group;                       //read from second column
 577
 578                                 //if this name is in the accnos file
 579                                 if (subset.count(name) != 0) {
 580                                         outGroup << name << '\t' << group << endl;
 581                                         subset.erase(name);
 582                                 }
 583
 584                                 m->gobble(inGroup);
 585                         }
 586                         inGroup.close();
 587                         outGroup.close();
 588
 589                         //sanity check
 590                         if (subset.size() != 0) {
 591                                 m->mothurOut("Your groupfile does not match your fasta file."); m->mothurOutEndLine();
 592                                 for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
 593                                         m->mothurOut("[ERROR]: " + *it + " is missing from your groupfile."); m->mothurOutEndLine();
 594                                 }
 595                         }
 596                 }
 597
 598                 return 0;
 599
 600         }
 601         catch(exception& e) {
 602                 m->errorOut(e, "SubSampleCommand", "getSubSampleFasta");
 603                 exit(1);
 604         }
 605 }
 606 //**********************************************************************************************************************
 607 int SubSampleCommand::getNames() {
 608         try {
 609
 610                 ifstream in;
 611                 m->openInputFile(fastafile, in);
 612
 613                 string thisname;
 614                 while(!in.eof()){
 615
 616                         if (m->control_pressed) { in.close(); return 0; }
 617
 618                         Sequence currSeq(in);
 619                         thisname = currSeq.getName();
 620
 621                         if (thisname != "") {
 622                                 vector<string> temp; temp.push_back(thisname);
 623                                 nameMap[thisname] = temp;
 624                                 names.push_back(thisname);
 625                         }
 626                         m->gobble(in);
 627                 }
 628                 in.close();
 629
 630                 return 0;
 631
 632         }
 633         catch(exception& e) {
 634                 m->errorOut(e, "SubSampleCommand", "getNames");
 635                 exit(1);
 636         }
 637 }
 638 //**********************************************************************************************************************
 639 int SubSampleCommand::readNames() {
 640         try {
 641
 642         nameMap.clear();
 643         m->readNames(namefile, nameMap);
 644
 645         //save names of all sequences
 646         map<string, vector<string> >::iterator it;
 647         for (it = nameMap.begin(); it != nameMap.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { names.push_back((it->second)[i]); } }
 648
 649                 return 0;
 650
 651         }
 652         catch(exception& e) {
 653                 m->errorOut(e, "SubSampleCommand", "readNames");
 654                 exit(1);
 655         }
 656 }
 657 //**********************************************************************************************************************
 658 int SubSampleCommand::getSubSampleShared() {
 659         try {
 660
 661                 InputData* input = new InputData(sharedfile, "sharedfile");
 662                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 663                 string lastLabel = lookup[0]->getLabel();
 664
 665                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 666                 set<string> processedLabels;
 667                 set<string> userLabels = labels;
 668
 669                 if (size == 0) { //user has not set size, set size = smallest samples size
 670                         size = lookup[0]->getNumSeqs();
 671                         for (int i = 1; i < lookup.size(); i++) {
 672                                 int thisSize = lookup[i]->getNumSeqs();
 673
 674                                 if (thisSize < size) {  size = thisSize;        }
 675                         }
 676                 }else {
 677                         m->clearGroups();
 678                         Groups.clear();
 679                         vector<SharedRAbundVector*> temp;
 680                         for (int i = 0; i < lookup.size(); i++) {
 681                                 if (lookup[i]->getNumSeqs() < size) {
 682                                         m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
 683                                         delete lookup[i];
 684                                 }else {
 685                                         Groups.push_back(lookup[i]->getGroup());
 686                                         temp.push_back(lookup[i]);
 687                                 }
 688                         }
 689                         lookup = temp;
 690                         m->setGroups(Groups);
 691                 }
 692
 693                 if (lookup.size() == 0) {  m->mothurOut("The size you selected is too large, skipping shared file."); m->mothurOutEndLine(); delete input; return 0; }
 694
 695                 m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
 696
 697                 //as long as you are not at the end of the file or done wih the lines you want
 698                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 699                         if (m->control_pressed) {  delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }  return 0;  }
 700
 701                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 702
 703                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 704
 705                                 processShared(lookup);
 706
 707                                 processedLabels.insert(lookup[0]->getLabel());
 708                                 userLabels.erase(lookup[0]->getLabel());
 709                         }
 710
 711                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 712                                 string saveLabel = lookup[0]->getLabel();
 713
 714                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 715
 716                                 lookup = input->getSharedRAbundVectors(lastLabel);
 717                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 718
 719                                 processShared(lookup);
 720
 721                                 processedLabels.insert(lookup[0]->getLabel());
 722                                 userLabels.erase(lookup[0]->getLabel());
 723
 724                                 //restore real lastlabel to save below
 725                                 lookup[0]->setLabel(saveLabel);
 726                         }
 727
 728                         lastLabel = lookup[0]->getLabel();
 729                         //prevent memory leak
 730                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 731
 732                         //get next line to process
 733                         lookup = input->getSharedRAbundVectors();
 734                 }
 735
 736
 737                 if (m->control_pressed) {   return 0;  }
 738
 739                 //output error messages about any remaining user labels
 740                 set<string>::iterator it;
 741                 bool needToRun = false;
 742                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 743                         m->mothurOut("Your file does not include the label " + *it);
 744                         if (processedLabels.count(lastLabel) != 1) {
 745                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 746                                 needToRun = true;
 747                         }else {
 748                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 749                         }
 750                 }
 751
 752                 //run last label if you need to
 753                 if (needToRun == true)  {
 754                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 755                         lookup = input->getSharedRAbundVectors(lastLabel);
 756
 757                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 758
 759                         processShared(lookup);
 760
 761                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 762                 }
 763
 764                 delete input;
 765
 766                 return 0;
 767
 768         }
 769         catch(exception& e) {
 770                 m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
 771                 exit(1);
 772         }
 773 }
 774 //**********************************************************************************************************************
 775 int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
 776         try {
 777
 778                 //save mothurOut's binLabels to restore for next label
 779                 vector<string> saveBinLabels = m->currentBinLabels;
 780
 781                 string thisOutputDir = outputDir;
 782                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 783                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + ".subsample" + m->getExtension(sharedfile);
 784
 785         SubSample sample;
 786         vector<string> subsampledLabels = sample.getSample(thislookup, size);
 787
 788         if (m->control_pressed) {  return 0; }
 789
 790         ofstream out;
 791                 m->openOutputFile(outputFileName, out);
 792                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 793
 794         m->currentBinLabels = subsampledLabels;
 795
 796                 thislookup[0]->printHeaders(out);
 797
 798                 for (int i = 0; i < thislookup.size(); i++) {
 799                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 800                         thislookup[i]->print(out);
 801                 }
 802                 out.close();
 803
 804
 805         //save mothurOut's binLabels to restore for next label
 806                 m->currentBinLabels = saveBinLabels;
 807
 808                 return 0;
 809
 810         }
 811         catch(exception& e) {
 812                 m->errorOut(e, "SubSampleCommand", "processShared");
 813                 exit(1);
 814         }
 815 }
 816 //**********************************************************************************************************************
 817 int SubSampleCommand::getSubSampleList() {
 818         try {
 819
 820                 string thisOutputDir = outputDir;
 821                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 822                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile);
 823
 824                 ofstream out;
 825                 m->openOutputFile(outputFileName, out);
 826                 outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 827
 828                 InputData* input = new InputData(listfile, "list");
 829                 ListVector* list = input->getListVector();
 830                 string lastLabel = list->getLabel();
 831
 832                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 833                 set<string> processedLabels;
 834                 set<string> userLabels = labels;
 835
 836                 ofstream outGroup;
 837                 GroupMap* groupMap;
 838                 if (groupfile != "") {
 839
 840                         groupMap = new GroupMap(groupfile);
 841                         groupMap->readMap();
 842
 843                         //takes care of user setting groupNames that are invalid or setting groups=all
 844                         SharedUtil* util = new SharedUtil();
 845                         vector<string> namesGroups = groupMap->getNamesOfGroups();
 846                         util->setGroups(Groups, namesGroups);
 847                         delete util;
 848
 849                         //create outputfiles
 850                         string groupOutputDir = outputDir;
 851                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
 852                         string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
 853
 854                         m->openOutputFile(groupOutputFileName, outGroup);
 855                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
 856
 857                         //file mismatch quit
 858                         if (list->getNumSeqs() != groupMap->getNumSeqs()) {
 859                                 m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 860                                 m->mothurOutEndLine();
 861                                 delete groupMap;
 862                                 delete list;
 863                                 delete input;
 864                                 out.close();
 865                                 outGroup.close();
 866                                 return 0;
 867                         }
 868                 }
 869
 870                 //make sure that if your picked groups size is not too big
 871                 if (persample) {
 872                         if (size == 0) { //user has not set size, set size = smallest samples size
 873                                 size = groupMap->getNumSeqs(Groups[0]);
 874                                 for (int i = 1; i < Groups.size(); i++) {
 875                                         int thisSize = groupMap->getNumSeqs(Groups[i]);
 876
 877                                         if (thisSize < size) {  size = thisSize;        }
 878                                 }
 879                         }else { //make sure size is not too large
 880                                 vector<string> newGroups;
 881                                 for (int i = 0; i < Groups.size(); i++) {
 882                                         int thisSize = groupMap->getNumSeqs(Groups[i]);
 883
 884                                         if (thisSize >= size) { newGroups.push_back(Groups[i]); }
 885                                         else {  m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
 886                                 }
 887                                 Groups = newGroups;
 888                         }
 889
 890                         m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
 891                 }else{
 892                         if (pickedGroups) {
 893                                 int total = 0;
 894                                 for(int i = 0; i < Groups.size(); i++) {
 895                                         total += groupMap->getNumSeqs(Groups[i]);
 896                                 }
 897
 898                                 if (size == 0) { //user has not set size, set size = 10% samples size
 899                                         size = int (total * 0.10);
 900                                 }
 901
 902                                 if (total < size) {
 903                                         m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
 904                                         size = int (total * 0.10);
 905                                 }
 906
 907                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
 908                         }else{
 909
 910                                 if (size == 0) { //user has not set size, set size = 10% samples size
 911                                         size = int (list->getNumSeqs() * 0.10);
 912                                 }
 913
 914                                 int thisSize = list->getNumSeqs();
 915                                 if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
 916                                         size = thisSize;
 917                                 }
 918
 919                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(list->getNumSeqs()) + "."); m->mothurOutEndLine();
 920                         }
 921                 }
 922
 923
 924                 //fill names
 925                 for (int i = 0; i < list->getNumBins(); i++) {
 926                         string binnames = list->get(i);
 927
 928                         //parse names
 929                         string individual = "";
 930                         int length = binnames.length();
 931                         for(int j=0;j<length;j++){
 932                                 if(binnames[j] == ','){
 933
 934                                         if (groupfile != "") { //if there is a groupfile given fill in group info
 935                                                 string group = groupMap->getGroup(individual);
 936                                                 if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 937
 938                                                 if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 939                                                         if (m->inUsersGroups(group, Groups)) {
 940                                                                 names.push_back(individual);
 941                                                         }
 942                                                 }else{
 943                                                         names.push_back(individual);
 944                                                 }
 945                                         }else{ //save everyone, group
 946                                                 names.push_back(individual);
 947                                         }
 948                                         individual = "";
 949                                 }
 950                                 else{
 951                                         individual += binnames[j];
 952                                 }
 953                         }
 954                         //save last name
 955                         if (groupfile != "") { //if there is a groupfile given fill in group info
 956                                 string group = groupMap->getGroup(individual);
 957                                 if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 958
 959                                 if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 960                                         if (m->inUsersGroups(group, Groups)) {
 961                                                 names.push_back(individual);
 962                                         }
 963                                 }else{
 964                                         names.push_back(individual);
 965                                 }
 966                         }else{ //save everyone, group
 967                                 names.push_back(individual);
 968                         }
 969                 }
 970
 971                 random_shuffle(names.begin(), names.end());
 972
 973                 //randomly select a subset of those names to include in the subsample
 974                 set<string> subset; //dont want repeat sequence names added
 975                 if (persample) {
 976                         //initialize counts
 977                         map<string, int> groupCounts;
 978                         map<string, int>::iterator itGroupCounts;
 979                         for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
 980
 981                         for (int j = 0; j < names.size(); j++) {
 982
 983                                 if (m->control_pressed) { return 0; }
 984
 985                                 string group = groupMap->getGroup(names[j]);
 986                                 if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 987                                 else{
 988                                         itGroupCounts = groupCounts.find(group);
 989                                         if (itGroupCounts != groupCounts.end()) {
 990                                                 if (groupCounts[group] < size) {        subset.insert(names[j]);        groupCounts[group]++; }
 991                                         }
 992                                 }
 993                         }
 994                 }else{
 995                         for (int j = 0; j < size; j++) {
 996
 997                                 if (m->control_pressed) { break; }
 998
 999                                 subset.insert(names[j]);
1000                         }
1001                 }
1002
1003                 if (groupfile != "") {
1004                         //write out new groupfile
1005                         for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
1006                                 string group = groupMap->getGroup(*it);
1007                                 if (group == "not found") { group = "NOTFOUND"; }
1008
1009                                 outGroup << *it << '\t' << group << endl;
1010                         }
1011                         outGroup.close(); delete groupMap;
1012                 }
1013
1014
1015                 //as long as you are not at the end of the file or done wih the lines you want
1016                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1017
1018                         if (m->control_pressed) {  delete list; delete input; out.close();  return 0;  }
1019
1020                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
1021
1022                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1023
1024                                 processList(list, out, subset);
1025
1026                                 processedLabels.insert(list->getLabel());
1027                                 userLabels.erase(list->getLabel());
1028                         }
1029
1030                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1031                                 string saveLabel = list->getLabel();
1032
1033                                 delete list;
1034
1035                                 list = input->getListVector(lastLabel);
1036                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1037
1038                                 processList(list, out, subset);
1039
1040                                 processedLabels.insert(list->getLabel());
1041                                 userLabels.erase(list->getLabel());
1042
1043                                 //restore real lastlabel to save below
1044                                 list->setLabel(saveLabel);
1045                         }
1046
1047                         lastLabel = list->getLabel();
1048
1049                         delete list; list = NULL;
1050
1051                         //get next line to process
1052                         list = input->getListVector();
1053                 }
1054
1055
1056                 if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); return 0;  }
1057
1058                 //output error messages about any remaining user labels
1059                 set<string>::iterator it;
1060                 bool needToRun = false;
1061                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1062                         m->mothurOut("Your file does not include the label " + *it);
1063                         if (processedLabels.count(lastLabel) != 1) {
1064                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1065                                 needToRun = true;
1066                         }else {
1067                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1068                         }
1069                 }
1070
1071                 //run last label if you need to
1072                 if (needToRun == true)  {
1073                         if (list != NULL) { delete list; }
1074
1075                         list = input->getListVector(lastLabel);
1076
1077                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1078
1079                         processList(list, out, subset);
1080
1081                         delete list; list = NULL;
1082                 }
1083
1084                 out.close();
1085                 if (list != NULL) { delete list; }
1086                 delete input;
1087
1088                 return 0;
1089
1090         }
1091         catch(exception& e) {
1092                 m->errorOut(e, "SubSampleCommand", "getSubSampleList");
1093                 exit(1);
1094         }
1095 }
1096 //**********************************************************************************************************************
1097 int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>& subset) {
1098         try {
1099
1100                 int numBins = list->getNumBins();
1101
1102                 ListVector* temp = new ListVector();
1103                 temp->setLabel(list->getLabel());
1104
1105                 for (int i = 0; i < numBins; i++) {
1106
1107                         if (m->control_pressed) { break; }
1108
1109                         string binnames = list->get(i);
1110
1111                         //parse names
1112                         string individual = "";
1113                         string newNames = "";
1114                         int length = binnames.length();
1115                         for(int j=0;j<length;j++){
1116                                 if(binnames[j] == ','){
1117                                         if (subset.count(individual) != 0) {  newNames += individual + ",";  }
1118                                         individual = "";
1119                                 }else{
1120                                         individual += binnames[j];
1121                                 }
1122                         }
1123                         if (subset.count(individual) != 0) {  newNames += individual + ",";  }
1124
1125
1126                         //if there are names in this bin add to new list
1127                         if (newNames != "") {
1128                                 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
1129                                 temp->push_back(newNames);
1130                         }
1131                 }
1132
1133                 delete list;
1134                 list = temp;
1135
1136                 if (m->control_pressed) { return 0; }
1137
1138                 list->print(out);
1139
1140                 return 0;
1141
1142         }
1143         catch(exception& e) {
1144                 m->errorOut(e, "SubSampleCommand", "processList");
1145                 exit(1);
1146         }
1147 }
1148 //**********************************************************************************************************************
1149 int SubSampleCommand::getSubSampleRabund() {
1150         try {
1151                 InputData* input = new InputData(rabundfile, "rabund");
1152                 RAbundVector* rabund = input->getRAbundVector();
1153                 string lastLabel = rabund->getLabel();
1154
1155                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1156                 set<string> processedLabels;
1157                 set<string> userLabels = labels;
1158
1159                 if (size == 0) { //user has not set size, set size = 10%
1160                         size = int((rabund->getNumSeqs()) * 0.10);
1161                 }else if (size > rabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping rabund file."); m->mothurOutEndLine(); delete input; delete rabund; return 0; }
1162
1163                 m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1164
1165                 string thisOutputDir = outputDir;
1166                 if (outputDir == "") {  thisOutputDir += m->hasPath(rabundfile);  }
1167                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile);
1168
1169                 ofstream out;
1170                 m->openOutputFile(outputFileName, out);
1171                 outputTypes["rabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1172
1173                 //as long as you are not at the end of the file or done wih the lines you want
1174                 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1175                         if (m->control_pressed) {  delete input; delete rabund; out.close(); return 0;  }
1176
1177                         if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
1178
1179                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1180
1181                                 processRabund(rabund, out);
1182
1183                                 processedLabels.insert(rabund->getLabel());
1184                                 userLabels.erase(rabund->getLabel());
1185                         }
1186
1187                         if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1188                                 string saveLabel = rabund->getLabel();
1189
1190                                 delete rabund;
1191
1192                                 rabund = input->getRAbundVector(lastLabel);
1193                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1194
1195                                 processRabund(rabund, out);
1196
1197                                 processedLabels.insert(rabund->getLabel());
1198                                 userLabels.erase(rabund->getLabel());
1199
1200                                 //restore real lastlabel to save below
1201                                 rabund->setLabel(saveLabel);
1202                         }
1203
1204                         lastLabel = rabund->getLabel();
1205
1206                         //prevent memory leak
1207                         delete rabund; rabund = NULL;
1208
1209                         //get next line to process
1210                         rabund = input->getRAbundVector();
1211                 }
1212
1213
1214                 if (m->control_pressed) {  out.close(); return 0;  }
1215
1216                 //output error messages about any remaining user labels
1217                 set<string>::iterator it;
1218                 bool needToRun = false;
1219                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1220                         m->mothurOut("Your file does not include the label " + *it);
1221                         if (processedLabels.count(lastLabel) != 1) {
1222                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1223                                 needToRun = true;
1224                         }else {
1225                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1226                         }
1227                 }
1228
1229                 //run last label if you need to
1230                 if (needToRun == true)  {
1231                         if (rabund != NULL) { delete rabund; }
1232
1233                         rabund = input->getRAbundVector(lastLabel);
1234
1235                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1236
1237                         processRabund(rabund, out);
1238
1239                         delete rabund;
1240                 }
1241
1242                 delete input;
1243                 out.close();
1244
1245                 return 0;
1246
1247         }
1248         catch(exception& e) {
1249                 m->errorOut(e, "SubSampleCommand", "getSubSampleRabund");
1250                 exit(1);
1251         }
1252 }
1253 //**********************************************************************************************************************
1254 int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) {
1255         try {
1256
1257                 int numBins = rabund->getNumBins();
1258                 int thisSize = rabund->getNumSeqs();
1259
1260                 if (thisSize != size) {
1261
1262                         OrderVector* order = new OrderVector();
1263                         for(int p=0;p<numBins;p++){
1264                                 for(int j=0;j<rabund->get(p);j++){
1265                                         order->push_back(p);
1266                                 }
1267                         }
1268                         random_shuffle(order->begin(), order->end());
1269
1270                         RAbundVector* temp = new RAbundVector(numBins);
1271                         temp->setLabel(rabund->getLabel());
1272
1273                         delete rabund;
1274                         rabund = temp;
1275
1276                         for (int j = 0; j < size; j++) {
1277
1278                                 if (m->control_pressed) { delete order; return 0; }
1279
1280                                 int bin = order->get(j);
1281
1282                                 int abund = rabund->get(bin);
1283                                 rabund->set(bin, (abund+1));
1284                         }
1285
1286                         delete order;
1287                 }
1288
1289                 if (m->control_pressed) { return 0; }
1290
1291                 rabund->print(out);
1292
1293                 return 0;
1294
1295         }
1296         catch(exception& e) {
1297                 m->errorOut(e, "SubSampleCommand", "processRabund");
1298                 exit(1);
1299         }
1300 }
1301 //**********************************************************************************************************************
1302 int SubSampleCommand::getSubSampleSabund() {
1303         try {
1304
1305                 InputData* input = new InputData(sabundfile, "sabund");
1306                 SAbundVector* sabund = input->getSAbundVector();
1307                 string lastLabel = sabund->getLabel();
1308
1309                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1310                 set<string> processedLabels;
1311                 set<string> userLabels = labels;
1312
1313                 if (size == 0) { //user has not set size, set size = 10%
1314                         size = int((sabund->getNumSeqs()) * 0.10);
1315                 }else if (size > sabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping sabund file."); m->mothurOutEndLine(); delete input; delete sabund; return 0; }
1316
1317
1318                 m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1319
1320                 string thisOutputDir = outputDir;
1321                 if (outputDir == "") {  thisOutputDir += m->hasPath(sabundfile);  }
1322                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile);
1323
1324                 ofstream out;
1325                 m->openOutputFile(outputFileName, out);
1326                 outputTypes["sabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1327
1328
1329                 //as long as you are not at the end of the file or done wih the lines you want
1330                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1331                         if (m->control_pressed) {  delete input; delete sabund; out.close(); return 0;  }
1332
1333                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
1334
1335                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1336
1337                                 processSabund(sabund, out);
1338
1339                                 processedLabels.insert(sabund->getLabel());
1340                                 userLabels.erase(sabund->getLabel());
1341                         }
1342
1343                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1344                                 string saveLabel = sabund->getLabel();
1345
1346                                 delete sabund;
1347
1348                                 sabund = input->getSAbundVector(lastLabel);
1349                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1350
1351                                 processSabund(sabund, out);
1352
1353                                 processedLabels.insert(sabund->getLabel());
1354                                 userLabels.erase(sabund->getLabel());
1355
1356                                 //restore real lastlabel to save below
1357                                 sabund->setLabel(saveLabel);
1358                         }
1359
1360                         lastLabel = sabund->getLabel();
1361
1362                         //prevent memory leak
1363                         delete sabund; sabund = NULL;
1364
1365                         //get next line to process
1366                         sabund = input->getSAbundVector();
1367                 }
1368
1369
1370                 if (m->control_pressed) {  out.close(); return 0;  }
1371
1372                 //output error messages about any remaining user labels
1373                 set<string>::iterator it;
1374                 bool needToRun = false;
1375                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1376                         m->mothurOut("Your file does not include the label " + *it);
1377                         if (processedLabels.count(lastLabel) != 1) {
1378                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1379                                 needToRun = true;
1380                         }else {
1381                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1382                         }
1383                 }
1384
1385                 //run last label if you need to
1386                 if (needToRun == true)  {
1387                         if (sabund != NULL) { delete sabund; }
1388
1389                         sabund = input->getSAbundVector(lastLabel);
1390
1391                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1392
1393                         processSabund(sabund, out);
1394
1395                         delete sabund;
1396                 }
1397
1398                 delete input;
1399                 out.close();
1400
1401                 return 0;
1402
1403         }
1404         catch(exception& e) {
1405                 m->errorOut(e, "SubSampleCommand", "getSubSampleSabund");
1406                 exit(1);
1407         }
1408 }
1409 //**********************************************************************************************************************
1410 int SubSampleCommand::processSabund(SAbundVector*& sabund, ofstream& out) {
1411         try {
1412
1413                 RAbundVector* rabund = new RAbundVector();
1414                 *rabund = sabund->getRAbundVector();
1415
1416                 int numBins = rabund->getNumBins();
1417                 int thisSize = rabund->getNumSeqs();
1418
1419                 if (thisSize != size) {
1420
1421                         OrderVector* order = new OrderVector();
1422                         for(int p=0;p<numBins;p++){
1423                                 for(int j=0;j<rabund->get(p);j++){
1424                                         order->push_back(p);
1425                                 }
1426                         }
1427                         random_shuffle(order->begin(), order->end());
1428
1429                         RAbundVector* temp = new RAbundVector(numBins);
1430                         temp->setLabel(rabund->getLabel());
1431
1432                         delete rabund;
1433                         rabund = temp;
1434
1435                         for (int j = 0; j < size; j++) {
1436
1437                                 if (m->control_pressed) { delete order; return 0; }
1438
1439                                 int bin = order->get(j);
1440
1441                                 int abund = rabund->get(bin);
1442                                 rabund->set(bin, (abund+1));
1443                         }
1444
1445                         delete order;
1446                 }
1447
1448                 if (m->control_pressed) { return 0; }
1449
1450                 delete sabund;
1451                 sabund = new SAbundVector();
1452                 *sabund = rabund->getSAbundVector();
1453                 delete rabund;
1454
1455                 sabund->print(out);
1456
1457                 return 0;
1458
1459         }
1460         catch(exception& e) {
1461                 m->errorOut(e, "SubSampleCommand", "processSabund");
1462                 exit(1);
1463         }
1464 }
1465 //**********************************************************************************************************************
1466
1467
1468