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::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pfasta);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  19                 CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(plist);
  20                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pshared);
  21                 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(prabund);
  22                 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(psabund);
  23                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  24                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  25                 CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
  26                 CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
  27                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  28                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  29
  30                 vector<string> myArray;
  31                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  32                 return myArray;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "SubSampleCommand", "setParameters");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 string SubSampleCommand::getHelpString(){
  41         try {
  42                 string helpString = "";
  43                 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";
  44                 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";
  45                 helpString += "The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n";
  46                 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";
  47                 helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
  48                 helpString += "The size parameter allows you indicate the size of your subsample.\n";
  49                 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";
  50                 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";
  51                 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";
  52                 helpString += "The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n";
  53                 helpString += "Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n";
  54                 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
  55                 helpString += "The sub.sample command outputs a .subsample file.\n";
  56                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
  57                 return helpString;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "SubSampleCommand", "getHelpString");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 SubSampleCommand::SubSampleCommand(){
  66         try {
  67                 abort = true; calledHelp = true;
  68                 setParameters();
  69                 vector<string> tempOutNames;
  70                 outputTypes["shared"] = tempOutNames;
  71                 outputTypes["list"] = tempOutNames;
  72                 outputTypes["rabund"] = tempOutNames;
  73                 outputTypes["sabund"] = tempOutNames;
  74                 outputTypes["fasta"] = tempOutNames;
  75                 outputTypes["name"] = tempOutNames;
  76                 outputTypes["group"] = tempOutNames;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
  80                 exit(1);
  81         }
  82 }
  83 //**********************************************************************************************************************
  84 SubSampleCommand::SubSampleCommand(string option) {
  85         try {
  86                 abort = false; calledHelp = false;
  87                 allLines = 1;
  88
  89                 //allow user to run help
  90                 if(option == "help") { help(); abort = true; calledHelp = true; }
  91
  92                 else {
  93                         vector<string> myArray = setParameters();
  94
  95                         OptionParser parser(option);
  96                         map<string,string> parameters = parser.getParameters();
  97
  98                         ValidParameters validParameter;
  99
 100                         //check to make sure all parameters are valid for command
 101                         map<string,string>::iterator it;
 102                         for (it = parameters.begin(); it != parameters.end(); it++) {
 103                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 104                         }
 105
 106                         //initialize outputTypes
 107                         vector<string> tempOutNames;
 108                         outputTypes["shared"] = tempOutNames;
 109                         outputTypes["list"] = tempOutNames;
 110                         outputTypes["rabund"] = tempOutNames;
 111                         outputTypes["sabund"] = tempOutNames;
 112                         outputTypes["fasta"] = tempOutNames;
 113                         outputTypes["name"] = tempOutNames;
 114                         outputTypes["group"] = tempOutNames;
 115
 116                         //if the user changes the output directory command factory will send this info to us in the output parameter
 117                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 118
 119                         //if the user changes the input directory command factory will send this info to us in the output parameter
 120                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 121                         if (inputDir == "not found"){   inputDir = "";          }
 122                         else {
 123                                 string path;
 124                                 it = parameters.find("list");
 125                                 //user has given a template file
 126                                 if(it != parameters.end()){
 127                                         path = m->hasPath(it->second);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 130                                 }
 131
 132                                 it = parameters.find("fasta");
 133                                 //user has given a template file
 134                                 if(it != parameters.end()){
 135                                         path = m->hasPath(it->second);
 136                                         //if the user has not given a path then, add inputdir. else leave path alone.
 137                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 138                                 }
 139
 140                                 it = parameters.find("shared");
 141                                 //user has given a template file
 142                                 if(it != parameters.end()){
 143                                         path = m->hasPath(it->second);
 144                                         //if the user has not given a path then, add inputdir. else leave path alone.
 145                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 146                                 }
 147
 148                                 it = parameters.find("group");
 149                                 //user has given a template file
 150                                 if(it != parameters.end()){
 151                                         path = m->hasPath(it->second);
 152                                         //if the user has not given a path then, add inputdir. else leave path alone.
 153                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 154                                 }
 155
 156                                 it = parameters.find("sabund");
 157                                 //user has given a template file
 158                                 if(it != parameters.end()){
 159                                         path = m->hasPath(it->second);
 160                                         //if the user has not given a path then, add inputdir. else leave path alone.
 161                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 162                                 }
 163
 164                                 it = parameters.find("rabund");
 165                                 //user has given a template file
 166                                 if(it != parameters.end()){
 167                                         path = m->hasPath(it->second);
 168                                         //if the user has not given a path then, add inputdir. else leave path alone.
 169                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 170                                 }
 171
 172                                 it = parameters.find("name");
 173                                 //user has given a template file
 174                                 if(it != parameters.end()){
 175                                         path = m->hasPath(it->second);
 176                                         //if the user has not given a path then, add inputdir. else leave path alone.
 177                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 178                                 }
 179                         }
 180
 181                         //check for required parameters
 182                         listfile = validParameter.validFile(parameters, "list", true);
 183                         if (listfile == "not open") { listfile = ""; abort = true; }
 184                         else if (listfile == "not found") { listfile = ""; }
 185
 186                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 187                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 188                         else if (sabundfile == "not found") { sabundfile = ""; }
 189
 190                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 191                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 192                         else if (rabundfile == "not found") { rabundfile = ""; }
 193
 194                         fastafile = validParameter.validFile(parameters, "fasta", true);
 195                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 196                         else if (fastafile == "not found") { fastafile = ""; }
 197
 198                         sharedfile = validParameter.validFile(parameters, "shared", true);
 199                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 200                         else if (sharedfile == "not found") { sharedfile = ""; }
 201
 202                         namefile = validParameter.validFile(parameters, "name", true);
 203                         if (namefile == "not open") { namefile = ""; abort = true; }
 204                         else if (namefile == "not found") { namefile = ""; }
 205
 206                         groupfile = validParameter.validFile(parameters, "group", true);
 207                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 208                         else if (groupfile == "not found") { groupfile = ""; }
 209
 210
 211                         //check for optional parameter and set defaults
 212                         // ...at some point should added some additional type checking...
 213                         label = validParameter.validFile(parameters, "label", false);
 214                         if (label == "not found") { label = ""; }
 215                         else {
 216                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 217                                 else { allLines = 1;  }
 218                         }
 219
 220                         groups = validParameter.validFile(parameters, "groups", false);
 221                         if (groups == "not found") { groups = ""; pickedGroups = false; }
 222                         else {
 223                                 pickedGroups = true;
 224                                 m->splitAtDash(groups, Groups);
 225                                 m->Groups = Groups;
 226                         }
 227
 228                         string temp = validParameter.validFile(parameters, "size", false);              if (temp == "not found"){       temp = "0";             }
 229                         convert(temp, size);
 230
 231                         temp = validParameter.validFile(parameters, "persample", false);                if (temp == "not found"){       temp = "f";             }
 232                         persample = m->isTrue(temp);
 233
 234                         if (groupfile == "") { persample = false; }
 235
 236                         if ((namefile != "") && (fastafile == "")) { m->mothurOut("You may only use a namefile with a fastafile."); m->mothurOutEndLine(); abort = true; }
 237
 238                         if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) {
 239                                 m->mothurOut("You must provide a fasta, list, sabund, rabund or shared file as an input file."); m->mothurOutEndLine(); abort = true; }
 240
 241                         if (pickedGroups && ((groupfile == "") && (sharedfile == ""))) {
 242                                 m->mothurOut("You cannot pick groups without a valid group file or shared file."); m->mothurOutEndLine(); abort = true; }
 243
 244                         if ((groupfile != "") && ((fastafile == "") && (listfile == ""))) {
 245                                 m->mothurOut("Group file only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
 246
 247                         if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) {
 248                                 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; }
 249
 250                 }
 251
 252         }
 253         catch(exception& e) {
 254                 m->errorOut(e, "SubSampleCommand", "SubSampleCommand");
 255                 exit(1);
 256         }
 257 }
 258 //**********************************************************************************************************************
 259
 260 int SubSampleCommand::execute(){
 261         try {
 262
 263                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 264
 265                 if (sharedfile != "")   {   getSubSampleShared();       }
 266                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 267
 268                 if (listfile != "")             {   getSubSampleList();         }
 269                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 270
 271                 if (rabundfile != "")   {   getSubSampleRabund();       }
 272                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 273
 274                 if (sabundfile != "")   {   getSubSampleSabund();       }
 275                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 276
 277                 if (fastafile != "")    {   getSubSampleFasta();        }
 278                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); return 0; } }
 279
 280                 //set fasta file as new current fastafile
 281                 string current = "";
 282                 itTypes = outputTypes.find("fasta");
 283                 if (itTypes != outputTypes.end()) {
 284                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 285                 }
 286
 287                 itTypes = outputTypes.find("name");
 288                 if (itTypes != outputTypes.end()) {
 289                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 290                 }
 291
 292                 itTypes = outputTypes.find("group");
 293                 if (itTypes != outputTypes.end()) {
 294                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 295                 }
 296
 297                 itTypes = outputTypes.find("list");
 298                 if (itTypes != outputTypes.end()) {
 299                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 300                 }
 301
 302                 itTypes = outputTypes.find("shared");
 303                 if (itTypes != outputTypes.end()) {
 304                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 305                 }
 306
 307                 itTypes = outputTypes.find("rabund");
 308                 if (itTypes != outputTypes.end()) {
 309                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 310                 }
 311
 312                 itTypes = outputTypes.find("sabund");
 313                 if (itTypes != outputTypes.end()) {
 314                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 315                 }
 316
 317
 318                 m->mothurOutEndLine();
 319                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 320                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 321                 m->mothurOutEndLine();
 322
 323                 return 0;
 324         }
 325         catch(exception& e) {
 326                 m->errorOut(e, "SubSampleCommand", "execute");
 327                 exit(1);
 328         }
 329 }
 330 //**********************************************************************************************************************
 331 int SubSampleCommand::getSubSampleFasta() {
 332         try {
 333
 334                 if (namefile != "") { readNames(); }    //fills names with all names in namefile.
 335                 else { getNames(); }//no name file, so get list of names to pick from
 336
 337                 GroupMap* groupMap;
 338                 if (groupfile != "") {
 339
 340                         groupMap = new GroupMap(groupfile);
 341                         groupMap->readMap();
 342
 343                         //takes care of user setting groupNames that are invalid or setting groups=all
 344                         SharedUtil* util = new SharedUtil();
 345                         util->setGroups(Groups, groupMap->namesOfGroups);
 346                         delete util;
 347
 348                         //file mismatch quit
 349                         if (names.size() != groupMap->getNumSeqs()) {
 350                                 m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 351                                 m->mothurOutEndLine();
 352                                 delete groupMap;
 353                                 return 0;
 354                         }
 355                 }
 356
 357                 if (m->control_pressed) { return 0; }
 358
 359                 string thisOutputDir = outputDir;
 360                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 361                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
 362
 363                 ofstream out;
 364                 m->openOutputFile(outputFileName, out);
 365                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 366
 367                 //make sure that if your picked groups size is not too big
 368                 int thisSize = names.size();
 369                 if (persample) {
 370                         if (size == 0) { //user has not set size, set size = smallest samples size
 371                                 size = groupMap->getNumSeqs(Groups[0]);
 372                                 for (int i = 1; i < Groups.size(); i++) {
 373                                         int thisSize = groupMap->getNumSeqs(Groups[i]);
 374
 375                                         if (thisSize < size) {  size = thisSize;        }
 376                                 }
 377                         }else { //make sure size is not too large
 378                                 int smallestSize = groupMap->getNumSeqs(Groups[0]);
 379                                 for (int i = 1; i < Groups.size(); i++) {
 380                                         int thisSize = groupMap->getNumSeqs(Groups[i]);
 381
 382                                         if (thisSize < smallestSize) {  smallestSize = thisSize;        }
 383                                 }
 384                                 if (smallestSize < size) { size = smallestSize; m->mothurOut("You have selected a size that is larger than your smallest sample, using your samllest sample size, " + toString(smallestSize) + "."); m->mothurOutEndLine(); }
 385                         }
 386
 387                         m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
 388                 }else {
 389                         if (pickedGroups) {
 390                                 int total = 0;
 391                                 for(int i = 0; i < Groups.size(); i++) {
 392                                         total += groupMap->getNumSeqs(Groups[i]);
 393                                 }
 394
 395                                 if (size == 0) { //user has not set size, set size = 10% samples size
 396                                         size = int (total * 0.10);
 397                                 }
 398
 399                                 if (total < size) {
 400                                         if (size != 0) {
 401                                                 m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
 402                                         }
 403                                         size = int (total * 0.10);
 404                                 }
 405
 406                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
 407                         }
 408
 409                         if (size == 0) { //user has not set size, set size = 10% samples size
 410                                 size = int (names.size() * 0.10);
 411                         }
 412
 413                         if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
 414                                 size = thisSize;
 415                         }
 416
 417                         if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); }
 418
 419                 }
 420                 random_shuffle(names.begin(), names.end());
 421
 422                 set<string> subset; //dont want repeat sequence names added
 423                 if (persample) {
 424                         for (int i = 0; i < Groups.size(); i++) {
 425
 426                                 //randomly select a subset of those names from this group to include in the subsample
 427                                 for (int j = 0; j < size; j++) {
 428
 429                                         if (m->control_pressed) { return 0; }
 430
 431                                         //get random sequence to add, making sure we have not already added it
 432                                         bool done = false;
 433                                         int myrand;
 434                                         while (!done) {
 435                                                 myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
 436
 437                                                 if (subset.count(names[myrand]) == 0)  {
 438
 439                                                         string group = groupMap->getGroup(names[myrand]);
 440                                                         if (group == "not found") { m->mothurOut("[ERROR]: " + names[myrand] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 441
 442                                                         if (group == Groups[i]) {       subset.insert(names[myrand]); break;    }
 443                                                 }
 444                                         }
 445                                 }
 446                         }
 447                 }else {
 448
 449                         //randomly select a subset of those names to include in the subsample
 450                         for (int j = 0; j < size; j++) {
 451
 452                                 if (m->control_pressed) { return 0; }
 453
 454                                 //get random sequence to add, making sure we have not already added it
 455                                 bool done = false;
 456                                 int myrand;
 457                                 while (!done) {
 458                                         myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
 459
 460                                         if (subset.count(names[myrand]) == 0)  {
 461
 462                                                 if (groupfile != "") { //if there is a groupfile given fill in group info
 463                                                         string group = groupMap->getGroup(names[myrand]);
 464                                                         if (group == "not found") { m->mothurOut("[ERROR]: " + names[myrand] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 465
 466                                                         if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 467                                                                 if (m->inUsersGroups(group, Groups)) {
 468                                                                         subset.insert(names[myrand]); break;
 469                                                                 }
 470                                                         }else{
 471                                                                 subset.insert(names[myrand]); break;
 472                                                         }
 473                                                 }else{ //save everyone, group
 474                                                         subset.insert(names[myrand]); break;
 475                                                 }
 476                                         }
 477                                 }
 478                         }
 479                 }
 480                 //read through fasta file outputting only the names on the subsample list
 481                 ifstream in;
 482                 m->openInputFile(fastafile, in);
 483
 484                 string thisname;
 485                 int count = 0;
 486                 map<string, vector<string> >::iterator itNameMap;
 487
 488                 while(!in.eof()){
 489
 490                         if (m->control_pressed) { in.close(); out.close();  return 0; }
 491
 492                         Sequence currSeq(in);
 493                         thisname = currSeq.getName();
 494
 495                         if (thisname != "") {
 496
 497                                 //does the subset contain a sequence that this sequence represents
 498                                 itNameMap = nameMap.find(thisname);
 499                                 if (itNameMap != nameMap.end()) {
 500                                         vector<string> nameRepresents = itNameMap->second;
 501
 502                                         for (int i = 0; i < nameRepresents.size(); i++){
 503                                                 if (subset.count(nameRepresents[i]) != 0) {
 504                                                         out << ">" << nameRepresents[i] << endl << currSeq.getAligned() << endl;
 505                                                         count++;
 506                                                 }
 507                                         }
 508                                 }else{
 509                                         m->mothurOut("[ERROR]: " + thisname + " is not in your namefile, please correct."); m->mothurOutEndLine();
 510                                 }
 511                         }
 512                         m->gobble(in);
 513                 }
 514                 in.close();
 515                 out.close();
 516
 517                 if (count != subset.size()) {
 518                         m->mothurOut("[ERROR]: The subset selected contained " + toString(subset.size()) + " sequences, but I only found " + toString(count) + " of those in the fastafile."); m->mothurOutEndLine();
 519                 }
 520
 521                 //if a groupfile is provided read through the group file only outputting the names on the subsample list
 522                 if (groupfile != "") {
 523
 524                         string groupOutputDir = outputDir;
 525                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
 526                         string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
 527
 528                         ofstream outGroup;
 529                         m->openOutputFile(groupOutputFileName, outGroup);
 530                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
 531
 532                         ifstream inGroup;
 533                         m->openInputFile(groupfile, inGroup);
 534                         string name, group;
 535
 536                         while(!inGroup.eof()){
 537
 538                                 if (m->control_pressed) { inGroup.close(); outGroup.close(); return 0; }
 539
 540                                 inGroup >> name;        m->gobble(inGroup);                     //read from first column
 541                                 inGroup >> group;                       //read from second column
 542
 543                                 //if this name is in the accnos file
 544                                 if (subset.count(name) != 0) {
 545                                         outGroup << name << '\t' << group << endl;
 546                                         subset.erase(name);
 547                                 }
 548
 549                                 m->gobble(inGroup);
 550                         }
 551                         inGroup.close();
 552                         outGroup.close();
 553
 554                         //sanity check
 555                         if (subset.size() != 0) {
 556                                 m->mothurOut("Your groupfile does not match your fasta file."); m->mothurOutEndLine();
 557                                 for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
 558                                         m->mothurOut("[ERROR]: " + *it + " is missing from your groupfile."); m->mothurOutEndLine();
 559                                 }
 560                         }
 561                 }
 562
 563                 return 0;
 564
 565         }
 566         catch(exception& e) {
 567                 m->errorOut(e, "SubSampleCommand", "getSubSampleFasta");
 568                 exit(1);
 569         }
 570 }
 571 //**********************************************************************************************************************
 572 int SubSampleCommand::getNames() {
 573         try {
 574
 575                 ifstream in;
 576                 m->openInputFile(fastafile, in);
 577
 578                 string thisname;
 579                 while(!in.eof()){
 580
 581                         if (m->control_pressed) { in.close(); return 0; }
 582
 583                         Sequence currSeq(in);
 584                         thisname = currSeq.getName();
 585
 586                         if (thisname != "") {
 587                                 vector<string> temp; temp.push_back(thisname);
 588                                 nameMap[thisname] = temp;
 589                                 names.push_back(thisname);
 590                         }
 591                         m->gobble(in);
 592                 }
 593                 in.close();
 594
 595                 return 0;
 596
 597         }
 598         catch(exception& e) {
 599                 m->errorOut(e, "SubSampleCommand", "getNames");
 600                 exit(1);
 601         }
 602 }
 603 //**********************************************************************************************************************
 604 int SubSampleCommand::readNames() {
 605         try {
 606
 607                 ifstream in;
 608                 m->openInputFile(namefile, in);
 609
 610                 string thisname, repnames;
 611                 map<string, vector<string> >::iterator it;
 612
 613                 while(!in.eof()){
 614
 615                         if (m->control_pressed) { in.close(); return 0; }
 616
 617                         in >> thisname;         m->gobble(in);          //read from first column
 618                         in >> repnames;                 //read from second column
 619
 620                         it = nameMap.find(thisname);
 621                         if (it == nameMap.end()) {
 622
 623                                 vector<string> splitRepNames;
 624                                 m->splitAtComma(repnames, splitRepNames);
 625
 626                                 nameMap[thisname] = splitRepNames;
 627                                 for (int i = 0; i < splitRepNames.size(); i++) { names.push_back(splitRepNames[i]); }
 628
 629                         }else{  m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine();  }
 630
 631                         m->gobble(in);
 632                 }
 633                 in.close();
 634
 635                 return 0;
 636
 637         }
 638         catch(exception& e) {
 639                 m->errorOut(e, "SubSampleCommand", "readNames");
 640                 exit(1);
 641         }
 642 }
 643 //**********************************************************************************************************************
 644 int SubSampleCommand::getSubSampleShared() {
 645         try {
 646
 647                 string thisOutputDir = outputDir;
 648                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 649                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "subsample" + m->getExtension(sharedfile);
 650
 651                 ofstream out;
 652                 m->openOutputFile(outputFileName, out);
 653                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 654
 655                 InputData* input = new InputData(sharedfile, "sharedfile");
 656                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 657                 string lastLabel = lookup[0]->getLabel();
 658
 659                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 660                 set<string> processedLabels;
 661                 set<string> userLabels = labels;
 662
 663                 if (size == 0) { //user has not set size, set size = smallest samples size
 664                         size = lookup[0]->getNumSeqs();
 665                         for (int i = 1; i < lookup.size(); i++) {
 666                                 int thisSize = lookup[i]->getNumSeqs();
 667
 668                                 if (thisSize < size) {  size = thisSize;        }
 669                         }
 670                 }
 671
 672                 m->mothurOut("Sampling " + toString(size) + " from " + toString(lookup[0]->getNumSeqs()) + "."); m->mothurOutEndLine();
 673
 674                 //as long as you are not at the end of the file or done wih the lines you want
 675                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 676                         if (m->control_pressed) {  delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; } out.close(); return 0;  }
 677
 678                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 679
 680                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 681
 682                                 processShared(lookup, out);
 683
 684                                 processedLabels.insert(lookup[0]->getLabel());
 685                                 userLabels.erase(lookup[0]->getLabel());
 686                         }
 687
 688                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 689                                 string saveLabel = lookup[0]->getLabel();
 690
 691                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 692
 693                                 lookup = input->getSharedRAbundVectors(lastLabel);
 694                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 695
 696                                 processShared(lookup, out);
 697
 698                                 processedLabels.insert(lookup[0]->getLabel());
 699                                 userLabels.erase(lookup[0]->getLabel());
 700
 701                                 //restore real lastlabel to save below
 702                                 lookup[0]->setLabel(saveLabel);
 703                         }
 704
 705                         lastLabel = lookup[0]->getLabel();
 706                         //prevent memory leak
 707                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 708
 709                         //get next line to process
 710                         lookup = input->getSharedRAbundVectors();
 711                 }
 712
 713
 714                 if (m->control_pressed) {  out.close(); return 0;  }
 715
 716                 //output error messages about any remaining user labels
 717                 set<string>::iterator it;
 718                 bool needToRun = false;
 719                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 720                         m->mothurOut("Your file does not include the label " + *it);
 721                         if (processedLabels.count(lastLabel) != 1) {
 722                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 723                                 needToRun = true;
 724                         }else {
 725                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 726                         }
 727                 }
 728
 729                 //run last label if you need to
 730                 if (needToRun == true)  {
 731                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 732                         lookup = input->getSharedRAbundVectors(lastLabel);
 733
 734                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 735
 736                         processShared(lookup, out);
 737
 738                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 739                 }
 740
 741                 delete input;
 742                 out.close();
 743
 744                 return 0;
 745
 746         }
 747         catch(exception& e) {
 748                 m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
 749                 exit(1);
 750         }
 751 }
 752 //**********************************************************************************************************************
 753 int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofstream& out) {
 754         try {
 755
 756                 int numBins = thislookup[0]->getNumBins();
 757                 for (int i = 0; i < thislookup.size(); i++) {
 758                         int thisSize = thislookup[i]->getNumSeqs();
 759
 760                         if (thisSize != size) {
 761
 762                                 string thisgroup = thislookup[i]->getGroup();
 763
 764                                 OrderVector* order = new OrderVector();
 765                                 for(int p=0;p<numBins;p++){
 766                                         for(int j=0;j<thislookup[i]->getAbundance(p);j++){
 767                                                 order->push_back(p);
 768                                         }
 769                                 }
 770                                 random_shuffle(order->begin(), order->end());
 771
 772                                 SharedRAbundVector* temp = new SharedRAbundVector(numBins);
 773                                 temp->setLabel(thislookup[i]->getLabel());
 774                                 temp->setGroup(thislookup[i]->getGroup());
 775
 776                                 delete thislookup[i];
 777                                 thislookup[i] = temp;
 778
 779
 780                                 for (int j = 0; j < size; j++) {
 781
 782                                         if (m->control_pressed) { delete order; return 0; }
 783
 784                                         //get random number to sample from order between 0 and thisSize-1.
 785                                         int myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
 786
 787                                         int bin = order->get(myrand);
 788
 789                                         int abund = thislookup[i]->getAbundance(bin);
 790                                         thislookup[i]->set(bin, (abund+1), thisgroup);
 791                                 }
 792                                 delete order;
 793                         }
 794                 }
 795
 796                 //subsampling may have created some otus with no sequences in them
 797                 eliminateZeroOTUS(thislookup);
 798
 799                 if (m->control_pressed) { return 0; }
 800
 801                 for (int i = 0; i < thislookup.size(); i++) {
 802                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 803                         thislookup[i]->print(out);
 804                 }
 805
 806                 return 0;
 807
 808         }
 809         catch(exception& e) {
 810                 m->errorOut(e, "SubSampleCommand", "processShared");
 811                 exit(1);
 812         }
 813 }
 814 //**********************************************************************************************************************
 815 int SubSampleCommand::getSubSampleList() {
 816         try {
 817
 818                 string thisOutputDir = outputDir;
 819                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 820                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile);
 821
 822                 ofstream out;
 823                 m->openOutputFile(outputFileName, out);
 824                 outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 825
 826                 InputData* input = new InputData(listfile, "list");
 827                 ListVector* list = input->getListVector();
 828                 string lastLabel = list->getLabel();
 829
 830                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 831                 set<string> processedLabels;
 832                 set<string> userLabels = labels;
 833
 834                 ofstream outGroup;
 835                 GroupMap* groupMap;
 836                 if (groupfile != "") {
 837
 838                         groupMap = new GroupMap(groupfile);
 839                         groupMap->readMap();
 840
 841                         //takes care of user setting groupNames that are invalid or setting groups=all
 842                         SharedUtil* util = new SharedUtil();
 843                         util->setGroups(Groups, groupMap->namesOfGroups);
 844                         delete util;
 845
 846                         //create outputfiles
 847                         string groupOutputDir = outputDir;
 848                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
 849                         string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
 850
 851                         m->openOutputFile(groupOutputFileName, outGroup);
 852                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
 853
 854                         //file mismatch quit
 855                         if (list->getNumSeqs() != groupMap->getNumSeqs()) {
 856                                 m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
 857                                 m->mothurOutEndLine();
 858                                 delete groupMap;
 859                                 delete list;
 860                                 delete input;
 861                                 out.close();
 862                                 outGroup.close();
 863                                 return 0;
 864                         }
 865                 }
 866
 867                 //make sure that if your picked groups size is not too big
 868                 if (persample) {
 869                         if (size == 0) { //user has not set size, set size = smallest samples size
 870                                 size = groupMap->getNumSeqs(Groups[0]);
 871                                 for (int i = 1; i < Groups.size(); i++) {
 872                                         int thisSize = groupMap->getNumSeqs(Groups[i]);
 873
 874                                         if (thisSize < size) {  size = thisSize;        }
 875                                 }
 876                         }else { //make sure size is not too large
 877                                 int smallestSize = groupMap->getNumSeqs(Groups[0]);
 878                                 for (int i = 1; i < Groups.size(); i++) {
 879                                         int thisSize = groupMap->getNumSeqs(Groups[i]);
 880
 881                                         if (thisSize < smallestSize) {  smallestSize = thisSize;        }
 882                                 }
 883                                 if (smallestSize < size) { size = smallestSize; m->mothurOut("You have selected a size that is larger than your smallest sample, using your samllest sample size, " + toString(smallestSize) + "."); m->mothurOutEndLine(); }
 884                         }
 885
 886                         m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
 887                 }else{
 888                         if (pickedGroups) {
 889                                 int total = 0;
 890                                 for(int i = 0; i < Groups.size(); i++) {
 891                                         total += groupMap->getNumSeqs(Groups[i]);
 892                                 }
 893
 894                                 if (size == 0) { //user has not set size, set size = 10% samples size
 895                                         size = int (total * 0.10);
 896                                 }
 897
 898                                 if (total < size) {
 899                                         m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
 900                                         size = int (total * 0.10);
 901                                 }
 902
 903                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
 904                         }else{
 905
 906                                 if (size == 0) { //user has not set size, set size = 10% samples size
 907                                         size = int (list->getNumSeqs() * 0.10);
 908                                 }
 909
 910                                 int thisSize = list->getNumSeqs();
 911                                 if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
 912                                         size = thisSize;
 913                                 }
 914
 915                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(list->getNumSeqs()) + "."); m->mothurOutEndLine();
 916                         }
 917                 }
 918
 919
 920                 //fill names
 921                 for (int i = 0; i < list->getNumBins(); i++) {
 922                         string binnames = list->get(i);
 923
 924                         //parse names
 925                         string individual = "";
 926                         int length = binnames.length();
 927                         for(int j=0;j<length;j++){
 928                                 if(binnames[j] == ','){
 929
 930                                         if (groupfile != "") { //if there is a groupfile given fill in group info
 931                                                 string group = groupMap->getGroup(individual);
 932                                                 if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 933
 934                                                 if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 935                                                         if (m->inUsersGroups(group, Groups)) {
 936                                                                 names.push_back(individual);
 937                                                         }
 938                                                 }else{
 939                                                         names.push_back(individual);
 940                                                 }
 941                                         }else{ //save everyone, group
 942                                                 names.push_back(individual);
 943                                         }
 944                                         individual = "";
 945                                 }
 946                                 else{
 947                                         individual += binnames[j];
 948                                 }
 949                         }
 950                         //save last name
 951                         if (groupfile != "") { //if there is a groupfile given fill in group info
 952                                 string group = groupMap->getGroup(individual);
 953                                 if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 954
 955                                 if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 956                                         if (m->inUsersGroups(group, Groups)) {
 957                                                 names.push_back(individual);
 958                                         }
 959                                 }else{
 960                                         names.push_back(individual);
 961                                 }
 962                         }else{ //save everyone, group
 963                                 names.push_back(individual);
 964                         }
 965                 }
 966
 967                 random_shuffle(names.begin(), names.end());
 968
 969                 //randomly select a subset of those names to include in the subsample
 970                 set<string> subset; //dont want repeat sequence names added
 971                 if (persample) {
 972                         for (int i = 0; i < Groups.size(); i++) {
 973
 974                                 for (int j = 0; j < size; j++) {
 975
 976                                         if (m->control_pressed) { break; }
 977
 978                                         //get random sequence to add, making sure we have not already added it
 979                                         bool done = false;
 980                                         int myrand;
 981                                         while (!done) {
 982                                                 myrand = int((float)(names.size()) * (float)(rand()) / ((float)RAND_MAX+1.0));
 983
 984                                                 if (subset.count(names[myrand]) == 0) { //you are not already added
 985                                                         if (groupMap->getGroup(names[myrand]) == Groups[i])  { subset.insert(names[myrand]); break;     }
 986                                                 }
 987                                         }
 988                                 }
 989                         }
 990                 }else{
 991                         for (int j = 0; j < size; j++) {
 992
 993                                 if (m->control_pressed) { break; }
 994
 995                                 //get random sequence to add, making sure we have not already added it
 996                                 bool done = false;
 997                                 int myrand;
 998                                 while (!done) {
 999                                         myrand = int((float)(names.size()) * (float)(rand()) / ((float)RAND_MAX+1.0));
1000
1001                                         if (subset.count(names[myrand]) == 0)  { subset.insert(names[myrand]); break;   }
1002                                 }
1003                         }
1004                 }
1005
1006                 if (groupfile != "") {
1007                         //write out new groupfile
1008                         for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
1009                                 string group = groupMap->getGroup(*it);
1010                                 if (group == "not found") { group = "NOTFOUND"; }
1011
1012                                 outGroup << *it << '\t' << group << endl;
1013                         }
1014                         outGroup.close(); delete groupMap;
1015                 }
1016
1017
1018                 //as long as you are not at the end of the file or done wih the lines you want
1019                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1020
1021                         if (m->control_pressed) {  delete list; delete input; out.close();  return 0;  }
1022
1023                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
1024
1025                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1026
1027                                 processList(list, out, subset);
1028
1029                                 processedLabels.insert(list->getLabel());
1030                                 userLabels.erase(list->getLabel());
1031                         }
1032
1033                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1034                                 string saveLabel = list->getLabel();
1035
1036                                 delete list;
1037
1038                                 list = input->getListVector(lastLabel);
1039                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1040
1041                                 processList(list, out, subset);
1042
1043                                 processedLabels.insert(list->getLabel());
1044                                 userLabels.erase(list->getLabel());
1045
1046                                 //restore real lastlabel to save below
1047                                 list->setLabel(saveLabel);
1048                         }
1049
1050                         lastLabel = list->getLabel();
1051
1052                         delete list; list = NULL;
1053
1054                         //get next line to process
1055                         list = input->getListVector();
1056                 }
1057
1058
1059                 if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); return 0;  }
1060
1061                 //output error messages about any remaining user labels
1062                 set<string>::iterator it;
1063                 bool needToRun = false;
1064                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1065                         m->mothurOut("Your file does not include the label " + *it);
1066                         if (processedLabels.count(lastLabel) != 1) {
1067                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1068                                 needToRun = true;
1069                         }else {
1070                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1071                         }
1072                 }
1073
1074                 //run last label if you need to
1075                 if (needToRun == true)  {
1076                         if (list != NULL) { delete list; }
1077
1078                         list = input->getListVector(lastLabel);
1079
1080                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1081
1082                         processList(list, out, subset);
1083
1084                         delete list; list = NULL;
1085                 }
1086
1087                 out.close();
1088                 if (list != NULL) { delete list; }
1089                 delete input;
1090
1091                 return 0;
1092
1093         }
1094         catch(exception& e) {
1095                 m->errorOut(e, "SubSampleCommand", "getSubSampleList");
1096                 exit(1);
1097         }
1098 }
1099 //**********************************************************************************************************************
1100 int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>& subset) {
1101         try {
1102
1103                 int numBins = list->getNumBins();
1104
1105                 ListVector* temp = new ListVector();
1106                 temp->setLabel(list->getLabel());
1107
1108                 for (int i = 0; i < numBins; i++) {
1109
1110                         if (m->control_pressed) { break; }
1111
1112                         string binnames = list->get(i);
1113
1114                         //parse names
1115                         string individual = "";
1116                         string newNames = "";
1117                         int length = binnames.length();
1118                         for(int j=0;j<length;j++){
1119                                 if(binnames[j] == ','){
1120                                         if (subset.count(individual) != 0) {  newNames += individual + ",";  }
1121                                         individual = "";
1122                                 }else{
1123                                         individual += binnames[j];
1124                                 }
1125                         }
1126                         if (subset.count(individual) != 0) {  newNames += individual;  }
1127
1128
1129                         //if there are names in this bin add to new list
1130                         if (newNames != "") {
1131                                 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
1132                                 temp->push_back(newNames);
1133                         }
1134                 }
1135
1136                 delete list;
1137                 list = temp;
1138
1139                 if (m->control_pressed) { return 0; }
1140
1141                 list->print(out);
1142
1143                 return 0;
1144
1145         }
1146         catch(exception& e) {
1147                 m->errorOut(e, "SubSampleCommand", "processList");
1148                 exit(1);
1149         }
1150 }
1151 //**********************************************************************************************************************
1152 int SubSampleCommand::getSubSampleRabund() {
1153         try {
1154
1155                 string thisOutputDir = outputDir;
1156                 if (outputDir == "") {  thisOutputDir += m->hasPath(rabundfile);  }
1157                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile);
1158
1159                 ofstream out;
1160                 m->openOutputFile(outputFileName, out);
1161                 outputTypes["rabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1162
1163                 InputData* input = new InputData(rabundfile, "rabund");
1164                 RAbundVector* rabund = input->getRAbundVector();
1165                 string lastLabel = rabund->getLabel();
1166
1167                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1168                 set<string> processedLabels;
1169                 set<string> userLabels = labels;
1170
1171                 if (size == 0) { //user has not set size, set size = 10%
1172                         size = int((rabund->getNumSeqs()) * 0.10);
1173                 }
1174
1175                 m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1176
1177                 //as long as you are not at the end of the file or done wih the lines you want
1178                 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1179                         if (m->control_pressed) {  delete input; delete rabund; out.close(); return 0;  }
1180
1181                         if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
1182
1183                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1184
1185                                 processRabund(rabund, out);
1186
1187                                 processedLabels.insert(rabund->getLabel());
1188                                 userLabels.erase(rabund->getLabel());
1189                         }
1190
1191                         if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1192                                 string saveLabel = rabund->getLabel();
1193
1194                                 delete rabund;
1195
1196                                 rabund = input->getRAbundVector(lastLabel);
1197                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1198
1199                                 processRabund(rabund, out);
1200
1201                                 processedLabels.insert(rabund->getLabel());
1202                                 userLabels.erase(rabund->getLabel());
1203
1204                                 //restore real lastlabel to save below
1205                                 rabund->setLabel(saveLabel);
1206                         }
1207
1208                         lastLabel = rabund->getLabel();
1209
1210                         //prevent memory leak
1211                         delete rabund; rabund = NULL;
1212
1213                         //get next line to process
1214                         rabund = input->getRAbundVector();
1215                 }
1216
1217
1218                 if (m->control_pressed) {  out.close(); return 0;  }
1219
1220                 //output error messages about any remaining user labels
1221                 set<string>::iterator it;
1222                 bool needToRun = false;
1223                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1224                         m->mothurOut("Your file does not include the label " + *it);
1225                         if (processedLabels.count(lastLabel) != 1) {
1226                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1227                                 needToRun = true;
1228                         }else {
1229                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1230                         }
1231                 }
1232
1233                 //run last label if you need to
1234                 if (needToRun == true)  {
1235                         if (rabund != NULL) { delete rabund; }
1236
1237                         rabund = input->getRAbundVector(lastLabel);
1238
1239                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1240
1241                         processRabund(rabund, out);
1242
1243                         delete rabund;
1244                 }
1245
1246                 delete input;
1247                 out.close();
1248
1249                 return 0;
1250
1251         }
1252         catch(exception& e) {
1253                 m->errorOut(e, "SubSampleCommand", "getSubSampleRabund");
1254                 exit(1);
1255         }
1256 }
1257 //**********************************************************************************************************************
1258 int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) {
1259         try {
1260
1261                 int numBins = rabund->getNumBins();
1262                 int thisSize = rabund->getNumSeqs();
1263
1264                 if (thisSize != size) {
1265
1266                         OrderVector* order = new OrderVector();
1267                         for(int p=0;p<numBins;p++){
1268                                 for(int j=0;j<rabund->get(p);j++){
1269                                         order->push_back(p);
1270                                 }
1271                         }
1272                         random_shuffle(order->begin(), order->end());
1273
1274                         RAbundVector* temp = new RAbundVector(numBins);
1275                         temp->setLabel(rabund->getLabel());
1276
1277                         delete rabund;
1278                         rabund = temp;
1279
1280                         for (int j = 0; j < size; j++) {
1281
1282                                 if (m->control_pressed) { delete order; return 0; }
1283
1284                                 //get random number to sample from order between 0 and thisSize-1.
1285                                 int myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
1286
1287                                 int bin = order->get(myrand);
1288
1289                                 int abund = rabund->get(bin);
1290                                 rabund->set(bin, (abund+1));
1291                         }
1292
1293                         delete order;
1294                 }
1295
1296                 if (m->control_pressed) { return 0; }
1297
1298                 rabund->print(out);
1299
1300                 return 0;
1301
1302         }
1303         catch(exception& e) {
1304                 m->errorOut(e, "SubSampleCommand", "processRabund");
1305                 exit(1);
1306         }
1307 }
1308 //**********************************************************************************************************************
1309 int SubSampleCommand::getSubSampleSabund() {
1310         try {
1311
1312                 string thisOutputDir = outputDir;
1313                 if (outputDir == "") {  thisOutputDir += m->hasPath(sabundfile);  }
1314                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile);
1315
1316                 ofstream out;
1317                 m->openOutputFile(outputFileName, out);
1318                 outputTypes["sabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1319
1320                 InputData* input = new InputData(sabundfile, "sabund");
1321                 SAbundVector* sabund = input->getSAbundVector();
1322                 string lastLabel = sabund->getLabel();
1323
1324                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1325                 set<string> processedLabels;
1326                 set<string> userLabels = labels;
1327
1328                 if (size == 0) { //user has not set size, set size = 10%
1329                         size = int((sabund->getNumSeqs()) * 0.10);
1330                 }
1331
1332                 m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1333
1334                 //as long as you are not at the end of the file or done wih the lines you want
1335                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1336                         if (m->control_pressed) {  delete input; delete sabund; out.close(); return 0;  }
1337
1338                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
1339
1340                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1341
1342                                 processSabund(sabund, out);
1343
1344                                 processedLabels.insert(sabund->getLabel());
1345                                 userLabels.erase(sabund->getLabel());
1346                         }
1347
1348                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1349                                 string saveLabel = sabund->getLabel();
1350
1351                                 delete sabund;
1352
1353                                 sabund = input->getSAbundVector(lastLabel);
1354                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1355
1356                                 processSabund(sabund, out);
1357
1358                                 processedLabels.insert(sabund->getLabel());
1359                                 userLabels.erase(sabund->getLabel());
1360
1361                                 //restore real lastlabel to save below
1362                                 sabund->setLabel(saveLabel);
1363                         }
1364
1365                         lastLabel = sabund->getLabel();
1366
1367                         //prevent memory leak
1368                         delete sabund; sabund = NULL;
1369
1370                         //get next line to process
1371                         sabund = input->getSAbundVector();
1372                 }
1373
1374
1375                 if (m->control_pressed) {  out.close(); return 0;  }
1376
1377                 //output error messages about any remaining user labels
1378                 set<string>::iterator it;
1379                 bool needToRun = false;
1380                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1381                         m->mothurOut("Your file does not include the label " + *it);
1382                         if (processedLabels.count(lastLabel) != 1) {
1383                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1384                                 needToRun = true;
1385                         }else {
1386                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1387                         }
1388                 }
1389
1390                 //run last label if you need to
1391                 if (needToRun == true)  {
1392                         if (sabund != NULL) { delete sabund; }
1393
1394                         sabund = input->getSAbundVector(lastLabel);
1395
1396                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1397
1398                         processSabund(sabund, out);
1399
1400                         delete sabund;
1401                 }
1402
1403                 delete input;
1404                 out.close();
1405
1406                 return 0;
1407
1408         }
1409         catch(exception& e) {
1410                 m->errorOut(e, "SubSampleCommand", "getSubSampleSabund");
1411                 exit(1);
1412         }
1413 }
1414 //**********************************************************************************************************************
1415 int SubSampleCommand::processSabund(SAbundVector*& sabund, ofstream& out) {
1416         try {
1417
1418                 RAbundVector* rabund = new RAbundVector();
1419                 *rabund = sabund->getRAbundVector();
1420
1421                 int numBins = rabund->getNumBins();
1422                 int thisSize = rabund->getNumSeqs();
1423
1424                 if (thisSize != size) {
1425
1426                         OrderVector* order = new OrderVector();
1427                         for(int p=0;p<numBins;p++){
1428                                 for(int j=0;j<rabund->get(p);j++){
1429                                         order->push_back(p);
1430                                 }
1431                         }
1432                         random_shuffle(order->begin(), order->end());
1433
1434                         RAbundVector* temp = new RAbundVector(numBins);
1435                         temp->setLabel(rabund->getLabel());
1436
1437                         delete rabund;
1438                         rabund = temp;
1439
1440                         for (int j = 0; j < size; j++) {
1441
1442                                 if (m->control_pressed) { delete order; return 0; }
1443
1444                                 //get random number to sample from order between 0 and thisSize-1.
1445                                 int myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
1446
1447                                 int bin = order->get(myrand);
1448
1449                                 int abund = rabund->get(bin);
1450                                 rabund->set(bin, (abund+1));
1451                         }
1452
1453                         delete order;
1454                 }
1455
1456                 if (m->control_pressed) { return 0; }
1457
1458                 delete sabund;
1459                 sabund = new SAbundVector();
1460                 *sabund = rabund->getSAbundVector();
1461                 delete rabund;
1462
1463                 sabund->print(out);
1464
1465                 return 0;
1466
1467         }
1468         catch(exception& e) {
1469                 m->errorOut(e, "SubSampleCommand", "processSabund");
1470                 exit(1);
1471         }
1472 }
1473 //**********************************************************************************************************************
1474 int SubSampleCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
1475         try {
1476
1477                 vector<SharedRAbundVector*> newLookup;
1478                 for (int i = 0; i < thislookup.size(); i++) {
1479                         SharedRAbundVector* temp = new SharedRAbundVector();
1480                         temp->setLabel(thislookup[i]->getLabel());
1481                         temp->setGroup(thislookup[i]->getGroup());
1482                         newLookup.push_back(temp);
1483                 }
1484
1485                 //for each bin
1486                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
1487                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
1488
1489                         //look at each sharedRabund and make sure they are not all zero
1490                         bool allZero = true;
1491                         for (int j = 0; j < thislookup.size(); j++) {
1492                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
1493                         }
1494
1495                         //if they are not all zero add this bin
1496                         if (!allZero) {
1497                                 for (int j = 0; j < thislookup.size(); j++) {
1498                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
1499                                 }
1500                         }
1501                 }
1502
1503                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
1504                 thislookup.clear();
1505
1506                 thislookup = newLookup;
1507
1508                 return 0;
1509
1510         }
1511         catch(exception& e) {
1512                 m->errorOut(e, "SubSampleCommand", "eliminateZeroOTUS");
1513                 exit(1);
1514         }
1515 }
1516
1517 //**********************************************************************************************************************
1518
1519
1520