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", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
  20         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
  21                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
  22                 CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(plist);
  23                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pshared);
  24                 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(prabund);
  25                 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(psabund);
  26                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  27                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  28                 CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
  29                 CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
  30                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  31                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  32
  33                 vector<string> myArray;
  34                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  35                 return myArray;
  36         }
  37         catch(exception& e) {
  38                 m->errorOut(e, "SubSampleCommand", "setParameters");
  39                 exit(1);
  40         }
  41 }
  42 //**********************************************************************************************************************
  43 string SubSampleCommand::getHelpString(){
  44         try {
  45                 string helpString = "";
  46                 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";
  47                 helpString += "The sub.sample command parameters are fasta, name, list, group, count, rabund, sabund, shared, groups, size, persample and label.  You must provide a fasta, list, sabund, rabund or shared file as an input file.\n";
  48                 helpString += "The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n";
  49                 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";
  50                 helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
  51                 helpString += "The size parameter allows you indicate the size of your subsample.\n";
  52                 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";
  53                 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";
  54                 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";
  55                 helpString += "The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n";
  56                 helpString += "Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n";
  57                 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
  58                 helpString += "The sub.sample command outputs a .subsample file.\n";
  59                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  60                 return helpString;
  61         }
  62         catch(exception& e) {
  63                 m->errorOut(e, "SubSampleCommand", "getHelpString");
  64                 exit(1);
  65         }
  66 }
  67 //**********************************************************************************************************************
  68 string SubSampleCommand::getOutputFileNameTag(string type, string inputName=""){
  69         try {
  70         string outputFileName = "";
  71                 map<string, vector<string> >::iterator it;
  72
  73         //is this a type this command creates
  74         it = outputTypes.find(type);
  75         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  76         else {
  77             if (type == "fasta")            {   outputFileName =  "subsample" + m->getExtension(inputName);   }
  78             else if (type == "sabund")    {   outputFileName =  "subsample" + m->getExtension(inputName);   }
  79             else if (type == "name")        {   outputFileName =  "subsample" + m->getExtension(inputName);   }
  80             else if (type == "count")        {   outputFileName =  "subsample" + m->getExtension(inputName);   }
  81             else if (type == "group")       {   outputFileName =  "subsample" + m->getExtension(inputName);   }
  82             else if (type == "list")        {   outputFileName =  "subsample" + m->getExtension(inputName);   }
  83             else if (type == "rabund")       {   outputFileName =  "subsample" + m->getExtension(inputName);   }
  84             else if (type == "shared") {   outputFileName =  "subsample" + m->getExtension(inputName);        }
  85             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  86         }
  87         return outputFileName;
  88         }
  89         catch(exception& e) {
  90                 m->errorOut(e, "SubSampleCommand", "getOutputFileNameTag");
  91                 exit(1);
  92         }
  93 }
  94
  95 //**********************************************************************************************************************
  96 SubSampleCommand::SubSampleCommand(){
  97         try {
  98                 abort = true; calledHelp = true;
  99                 setParameters();
 100                 vector<string> tempOutNames;
 101                 outputTypes["shared"] = tempOutNames;
 102                 outputTypes["list"] = tempOutNames;
 103                 outputTypes["rabund"] = tempOutNames;
 104                 outputTypes["sabund"] = tempOutNames;
 105                 outputTypes["fasta"] = tempOutNames;
 106                 outputTypes["name"] = tempOutNames;
 107                 outputTypes["group"] = tempOutNames;
 108         outputTypes["count"] = tempOutNames;
 109         }
 110         catch(exception& e) {
 111                 m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
 112                 exit(1);
 113         }
 114 }
 115 //**********************************************************************************************************************
 116 SubSampleCommand::SubSampleCommand(string option) {
 117         try {
 118                 abort = false; calledHelp = false;
 119                 allLines = 1;
 120
 121                 //allow user to run help
 122                 if(option == "help") { help(); abort = true; calledHelp = true; }
 123                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 124
 125                 else {
 126                         vector<string> myArray = setParameters();
 127
 128                         OptionParser parser(option);
 129                         map<string,string> parameters = parser.getParameters();
 130
 131                         ValidParameters validParameter;
 132
 133                         //check to make sure all parameters are valid for command
 134                         map<string,string>::iterator it;
 135                         for (it = parameters.begin(); it != parameters.end(); it++) {
 136                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 137                         }
 138
 139                         //initialize outputTypes
 140                         vector<string> tempOutNames;
 141                         outputTypes["shared"] = tempOutNames;
 142                         outputTypes["list"] = tempOutNames;
 143                         outputTypes["rabund"] = tempOutNames;
 144                         outputTypes["sabund"] = tempOutNames;
 145                         outputTypes["fasta"] = tempOutNames;
 146                         outputTypes["name"] = tempOutNames;
 147                         outputTypes["group"] = tempOutNames;
 148             outputTypes["count"] = tempOutNames;
 149
 150                         //if the user changes the output directory command factory will send this info to us in the output parameter
 151                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 152
 153                         //if the user changes the input directory command factory will send this info to us in the output parameter
 154                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 155                         if (inputDir == "not found"){   inputDir = "";          }
 156                         else {
 157                                 string path;
 158                                 it = parameters.find("list");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 164                                 }
 165
 166                                 it = parameters.find("fasta");
 167                                 //user has given a template file
 168                                 if(it != parameters.end()){
 169                                         path = m->hasPath(it->second);
 170                                         //if the user has not given a path then, add inputdir. else leave path alone.
 171                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 172                                 }
 173
 174                                 it = parameters.find("shared");
 175                                 //user has given a template file
 176                                 if(it != parameters.end()){
 177                                         path = m->hasPath(it->second);
 178                                         //if the user has not given a path then, add inputdir. else leave path alone.
 179                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 180                                 }
 181
 182                                 it = parameters.find("group");
 183                                 //user has given a template file
 184                                 if(it != parameters.end()){
 185                                         path = m->hasPath(it->second);
 186                                         //if the user has not given a path then, add inputdir. else leave path alone.
 187                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 188                                 }
 189
 190                                 it = parameters.find("sabund");
 191                                 //user has given a template file
 192                                 if(it != parameters.end()){
 193                                         path = m->hasPath(it->second);
 194                                         //if the user has not given a path then, add inputdir. else leave path alone.
 195                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 196                                 }
 197
 198                                 it = parameters.find("rabund");
 199                                 //user has given a template file
 200                                 if(it != parameters.end()){
 201                                         path = m->hasPath(it->second);
 202                                         //if the user has not given a path then, add inputdir. else leave path alone.
 203                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 204                                 }
 205
 206                                 it = parameters.find("name");
 207                                 //user has given a template file
 208                                 if(it != parameters.end()){
 209                                         path = m->hasPath(it->second);
 210                                         //if the user has not given a path then, add inputdir. else leave path alone.
 211                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 212                                 }
 213
 214                 it = parameters.find("count");
 215                                 //user has given a template file
 216                                 if(it != parameters.end()){
 217                                         path = m->hasPath(it->second);
 218                                         //if the user has not given a path then, add inputdir. else leave path alone.
 219                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 220                                 }
 221                         }
 222
 223                         //check for required parameters
 224                         listfile = validParameter.validFile(parameters, "list", true);
 225                         if (listfile == "not open") { listfile = ""; abort = true; }
 226                         else if (listfile == "not found") { listfile = ""; }
 227                         else { m->setListFile(listfile); }
 228
 229                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 230                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 231                         else if (sabundfile == "not found") { sabundfile = ""; }
 232                         else { m->setSabundFile(sabundfile); }
 233
 234                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 235                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 236                         else if (rabundfile == "not found") { rabundfile = ""; }
 237                         else { m->setRabundFile(rabundfile); }
 238
 239                         fastafile = validParameter.validFile(parameters, "fasta", true);
 240                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 241                         else if (fastafile == "not found") { fastafile = ""; }
 242                         else { m->setFastaFile(fastafile); }
 243
 244                         sharedfile = validParameter.validFile(parameters, "shared", true);
 245                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 246                         else if (sharedfile == "not found") { sharedfile = ""; }
 247                         else { m->setSharedFile(sharedfile); }
 248
 249                         namefile = validParameter.validFile(parameters, "name", true);
 250                         if (namefile == "not open") { namefile = ""; abort = true; }
 251                         else if (namefile == "not found") { namefile = ""; }
 252                         else { m->setNameFile(namefile); }
 253
 254                         groupfile = validParameter.validFile(parameters, "group", true);
 255                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 256                         else if (groupfile == "not found") { groupfile = ""; }
 257                         else { m->setGroupFile(groupfile); }
 258
 259             countfile = validParameter.validFile(parameters, "count", true);
 260                         if (countfile == "not open") { countfile = ""; abort = true; }
 261                         else if (countfile == "not found") { countfile = "";  }
 262                         else {
 263                 m->setCountTableFile(countfile);
 264                 ct.readTable(countfile);
 265             }
 266
 267             if ((namefile != "") && (countfile != "")) {
 268                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 269             }
 270
 271             if ((groupfile != "") && (countfile != "")) {
 272                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 273             }
 274
 275                         //check for optional parameter and set defaults
 276                         // ...at some point should added some additional type checking...
 277                         label = validParameter.validFile(parameters, "label", false);
 278                         if (label == "not found") { label = ""; }
 279                         else {
 280                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 281                                 else { allLines = 1;  }
 282                         }
 283
 284                         groups = validParameter.validFile(parameters, "groups", false);
 285                         if (groups == "not found") { groups = ""; pickedGroups = false; }
 286                         else {
 287                                 pickedGroups = true;
 288                                 m->splitAtDash(groups, Groups);
 289                                 m->setGroups(Groups);
 290                         }
 291
 292                         string temp = validParameter.validFile(parameters, "size", false);              if (temp == "not found"){       temp = "0";             }
 293                         m->mothurConvert(temp, size);
 294
 295                         temp = validParameter.validFile(parameters, "persample", false);                if (temp == "not found"){       temp = "f";             }
 296                         persample = m->isTrue(temp);
 297
 298                         if ((groupfile == "") && (countfile == "")) { persample = false; }
 299             if (countfile != "") {
 300                 if (!ct.hasGroupInfo()) {
 301                     persample = false;
 302                     if (pickedGroups) { m->mothurOut("You cannot pick groups without group info in your count file."); m->mothurOutEndLine(); abort = true; }
 303                 }
 304             }
 305
 306                         if ((namefile != "") && (fastafile == "")) { m->mothurOut("You may only use a namefile with a fastafile."); m->mothurOutEndLine(); abort = true; }
 307
 308                         if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) {
 309                                 m->mothurOut("You must provide a fasta, list, sabund, rabund or shared file as an input file."); m->mothurOutEndLine(); abort = true; }
 310
 311                         if (pickedGroups && ((groupfile == "") && (sharedfile == "") && (countfile == ""))) {
 312                                 m->mothurOut("You cannot pick groups without a valid group, count or shared file."); m->mothurOutEndLine(); abort = true; }
 313
 314                         if (((groupfile != "") || (countfile != "")) && ((fastafile == "") && (listfile == ""))) {
 315                                 m->mothurOut("Group or count files are only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
 316
 317                         if (((groupfile != "") || (countfile != "")) && ((fastafile != "") && (listfile != ""))) {
 318                                 m->mothurOut("A new group or count file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
 319
 320             if (countfile == "") {
 321                 if ((fastafile != "") && (namefile == "")) {
 322                     vector<string> files; files.push_back(fastafile);
 323                     parser.getNameFile(files);
 324                 }
 325             }
 326                 }
 327
 328         }
 329         catch(exception& e) {
 330                 m->errorOut(e, "SubSampleCommand", "SubSampleCommand");
 331                 exit(1);
 332         }
 333 }
 334 //**********************************************************************************************************************
 335
 336 int SubSampleCommand::execute(){
 337         try {
 338
 339                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 340
 341                 if (sharedfile != "")   {   getSubSampleShared();       }
 342                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 343
 344                 if (listfile != "")             {   getSubSampleList();         }
 345                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 346
 347                 if (rabundfile != "")   {   getSubSampleRabund();       }
 348                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 349
 350                 if (sabundfile != "")   {   getSubSampleSabund();       }
 351                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 352
 353                 if (fastafile != "")    {   getSubSampleFasta();        }
 354                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 355
 356                 //set fasta file as new current fastafile
 357                 string current = "";
 358                 itTypes = outputTypes.find("fasta");
 359                 if (itTypes != outputTypes.end()) {
 360                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 361                 }
 362
 363                 itTypes = outputTypes.find("name");
 364                 if (itTypes != outputTypes.end()) {
 365                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 366                 }
 367
 368                 itTypes = outputTypes.find("group");
 369                 if (itTypes != outputTypes.end()) {
 370                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 371                 }
 372
 373                 itTypes = outputTypes.find("list");
 374                 if (itTypes != outputTypes.end()) {
 375                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 376                 }
 377
 378                 itTypes = outputTypes.find("shared");
 379                 if (itTypes != outputTypes.end()) {
 380                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 381                 }
 382
 383                 itTypes = outputTypes.find("rabund");
 384                 if (itTypes != outputTypes.end()) {
 385                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 386                 }
 387
 388                 itTypes = outputTypes.find("sabund");
 389                 if (itTypes != outputTypes.end()) {
 390                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 391                 }
 392
 393         itTypes = outputTypes.find("count");
 394                 if (itTypes != outputTypes.end()) {
 395                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 396                 }
 397
 398
 399                 m->mothurOutEndLine();
 400                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 401                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 402                 m->mothurOutEndLine();
 403
 404                 return 0;
 405         }
 406         catch(exception& e) {
 407                 m->errorOut(e, "SubSampleCommand", "execute");
 408                 exit(1);
 409         }
 410 }
 411 //**********************************************************************************************************************
 412 int SubSampleCommand::getSubSampleFasta() {
 413         try {
 414
 415                 if (namefile != "") { readNames(); }    //fills names with all names in namefile.
 416                 else { getNames(); }//no name file, so get list of names to pick from
 417
 418                 GroupMap groupMap;
 419                 if (groupfile != "") {
 420                         groupMap.readMap(groupfile);
 421
 422                         //takes care of user setting groupNames that are invalid or setting groups=all
 423                         SharedUtil util;
 424                         vector<string> namesGroups = groupMap.getNamesOfGroups();
 425                         util.setGroups(Groups, namesGroups);
 426
 427                         //file mismatch quit
 428                         if (names.size() != groupMap.getNumSeqs()) {
 429                                 m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap.getNumSeqs()) + ", please correct.");
 430                                 m->mothurOutEndLine();
 431                                 return 0;
 432                         }
 433                 }else if (countfile != "") {
 434             if (ct.hasGroupInfo()) {
 435                 SharedUtil util;
 436                 vector<string> namesGroups = ct.getNamesOfGroups();
 437                 util.setGroups(Groups, namesGroups);
 438             }
 439
 440             //file mismatch quit
 441                         if (names.size() != ct.getNumUniqueSeqs()) {
 442                                 m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your count file contains " + toString(ct.getNumUniqueSeqs()) + " unique sequences, please correct.");
 443                                 m->mothurOutEndLine();
 444                                 return 0;
 445                         }
 446         }
 447
 448                 if (m->control_pressed) { return 0; }
 449
 450                 //make sure that if your picked groups size is not too big
 451                 int thisSize = 0;
 452         if (countfile == "") { thisSize = names.size();  }
 453         else {  thisSize = ct. getNumSeqs();  }  //all seqs not just unique
 454
 455                 if (persample) {
 456                         if (size == 0) { //user has not set size, set size = smallest samples size
 457                                 if (countfile == "") { size = groupMap.getNumSeqs(Groups[0]); }
 458                 else {  size = ct.getGroupCount(Groups[0]);  }
 459
 460                                 for (int i = 1; i < Groups.size(); i++) {
 461                                         int thisSize = 0;
 462                     if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
 463                     else {  thisSize = ct.getGroupCount(Groups[i]);  }
 464
 465                                         if (thisSize < size) {  size = thisSize;        }
 466                                 }
 467                         }else { //make sure size is not too large
 468                                 vector<string> newGroups;
 469                                 for (int i = 0; i < Groups.size(); i++) {
 470                                         int thisSize = 0;
 471                     if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
 472                     else {  thisSize = ct.getGroupCount(Groups[i]);  }
 473
 474                                         if (thisSize >= size) { newGroups.push_back(Groups[i]); }
 475                                         else {  m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
 476                                 }
 477                                 Groups = newGroups;
 478                 if (newGroups.size() == 0) {  m->mothurOut("[ERROR]: all groups removed."); m->mothurOutEndLine(); m->control_pressed = true; }
 479                         }
 480
 481                         m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
 482                 }else {
 483                         if (pickedGroups) {
 484                                 int total = 0;
 485                                 for(int i = 0; i < Groups.size(); i++) {
 486                     if (countfile == "") { total += groupMap.getNumSeqs(Groups[i]); }
 487                     else {  total += ct.getGroupCount(Groups[i]);  }
 488                                 }
 489
 490                                 if (size == 0) { //user has not set size, set size = 10% samples size
 491                                         size = int (total * 0.10);
 492                                 }
 493
 494                                 if (total < size) {
 495                                         if (size != 0) {
 496                                                 m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
 497                                         }
 498                                         size = int (total * 0.10);
 499                                 }
 500
 501                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
 502                         }
 503
 504                         if (size == 0) { //user has not set size, set size = 10% samples size
 505                                 if (countfile == "") {  size = int (names.size() * 0.10); }
 506                 else {  size = int (ct.getNumSeqs() * 0.10); }
 507                         }
 508
 509
 510             if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
 511                     size = thisSize;
 512             }
 513
 514             if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); }
 515
 516                 }
 517                 random_shuffle(names.begin(), names.end());
 518
 519                 set<string> subset; //dont want repeat sequence names added
 520                 if (persample) {
 521             if (countfile == "") {
 522                 //initialize counts
 523                 map<string, int> groupCounts;
 524                 map<string, int>::iterator itGroupCounts;
 525                 for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
 526
 527                 for (int j = 0; j < names.size(); j++) {
 528
 529                     if (m->control_pressed) { return 0; }
 530
 531                     string group = groupMap.getGroup(names[j]);
 532                     if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 533                     else{
 534                         itGroupCounts = groupCounts.find(group);
 535                         if (itGroupCounts != groupCounts.end()) {
 536                             if (groupCounts[group] < size) {    subset.insert(names[j]);        groupCounts[group]++; }
 537                         }
 538                     }
 539                 }
 540             }else {
 541                 SubSample sample;
 542                 CountTable sampledCt = sample.getSample(ct, size, Groups);
 543                 vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
 544                 for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
 545
 546                 string countOutputDir = outputDir;
 547                 if (outputDir == "") {  countOutputDir += m->hasPath(countfile);  }
 548                 string countOutputFileName = countOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
 549                 outputTypes["count"].push_back(countOutputFileName);  outputNames.push_back(countOutputFileName);
 550                 sampledCt.printTable(countOutputFileName);
 551             }
 552                 }else {
 553                         if (countfile == "") {
 554                 //randomly select a subset of those names to include in the subsample
 555                 //since names was randomly shuffled just grab the next one
 556                 for (int j = 0; j < names.size(); j++) {
 557
 558                     if (m->control_pressed) { return 0; }
 559
 560                     if (groupfile != "") { //if there is a groupfile given fill in group info
 561                         string group = groupMap.getGroup(names[j]);
 562                         if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 563
 564                         if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 565                             if (m->inUsersGroups(group, Groups)) {  subset.insert(names[j]); }
 566                         }else{  subset.insert(names[j]); }
 567                     }else{ //save everyone, group
 568                         subset.insert(names[j]);
 569                     }
 570
 571                     //do we have enough??
 572                     if (subset.size() == size) { break; }
 573                 }
 574             }else {
 575                 SubSample sample;
 576                 CountTable sampledCt = sample.getSample(ct, size, Groups, pickedGroups);
 577                 vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
 578                 for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
 579
 580                 string countOutputDir = outputDir;
 581                 if (outputDir == "") {  countOutputDir += m->hasPath(countfile);  }
 582                 string countOutputFileName = countOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
 583                 outputTypes["count"].push_back(countOutputFileName);  outputNames.push_back(countOutputFileName);
 584                 sampledCt.printTable(countOutputFileName);
 585             }
 586                 }
 587
 588                 if (subset.size() == 0) {  m->mothurOut("The size you selected is too large, skipping fasta file."); m->mothurOutEndLine();  return 0; }
 589
 590                 string thisOutputDir = outputDir;
 591                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 592                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 593                 ofstream out;
 594                 m->openOutputFile(outputFileName, out);
 595
 596                 //read through fasta file outputting only the names on the subsample list
 597                 ifstream in;
 598                 m->openInputFile(fastafile, in);
 599
 600                 string thisname;
 601                 int count = 0;
 602                 map<string, vector<string> >::iterator itNameMap;
 603
 604                 while(!in.eof()){
 605
 606                         if (m->control_pressed) { in.close(); out.close();  return 0; }
 607
 608                         Sequence currSeq(in);
 609                         thisname = currSeq.getName();
 610
 611                         if (thisname != "") {
 612
 613                                 //does the subset contain a sequence that this sequence represents
 614                                 itNameMap = nameMap.find(thisname);
 615                                 if (itNameMap != nameMap.end()) {
 616                                         vector<string> nameRepresents = itNameMap->second;
 617
 618                                         for (int i = 0; i < nameRepresents.size(); i++){
 619                                                 if (subset.count(nameRepresents[i]) != 0) {
 620                                                         out << ">" << nameRepresents[i] << endl << currSeq.getAligned() << endl;
 621                                                         count++;
 622                                                 }
 623                                         }
 624                                 }else{
 625                                         m->mothurOut("[ERROR]: " + thisname + " is not in your namefile, please correct."); m->mothurOutEndLine();
 626                                 }
 627                         }
 628                         m->gobble(in);
 629                 }
 630                 in.close();
 631                 out.close();
 632
 633                 if (count != subset.size()) {
 634                         m->mothurOut("[ERROR]: The subset selected contained " + toString(subset.size()) + " sequences, but I only found " + toString(count) + " of those in the fastafile."); m->mothurOutEndLine();
 635                 }
 636
 637                 if (namefile != "") {
 638                         m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
 639
 640             string outputNameFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 641                         //use unique.seqs to create new name and fastafile
 642                         string inputString = "fasta=" + outputFileName;
 643                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 644                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 645                         m->mothurCalling = true;
 646
 647                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 648                         uniqueCommand->execute();
 649
 650                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 651
 652                         delete uniqueCommand;
 653                         m->mothurCalling = false;
 654
 655             m->renameFile(filenames["name"][0], outputNameFileName);
 656             m->renameFile(filenames["fasta"][0], outputFileName);
 657
 658                         outputTypes["name"].push_back(outputNameFileName);  outputNames.push_back(outputNameFileName);
 659
 660                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 661
 662                         m->mothurOut("Done."); m->mothurOutEndLine();
 663                 }
 664
 665                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 666
 667                 //if a groupfile is provided read through the group file only outputting the names on the subsample list
 668                 if (groupfile != "") {
 669
 670                         string groupOutputDir = outputDir;
 671                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
 672                         string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 673
 674                         ofstream outGroup;
 675                         m->openOutputFile(groupOutputFileName, outGroup);
 676                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
 677
 678                         ifstream inGroup;
 679                         m->openInputFile(groupfile, inGroup);
 680                         string name, group;
 681
 682                         while(!inGroup.eof()){
 683
 684                                 if (m->control_pressed) { inGroup.close(); outGroup.close(); return 0; }
 685
 686                                 inGroup >> name;        m->gobble(inGroup);                     //read from first column
 687                                 inGroup >> group;                       //read from second column
 688
 689                                 //if this name is in the accnos file
 690                                 if (subset.count(name) != 0) {
 691                                         outGroup << name << '\t' << group << endl;
 692                                         subset.erase(name);
 693                                 }
 694
 695                                 m->gobble(inGroup);
 696                         }
 697                         inGroup.close();
 698                         outGroup.close();
 699
 700                         //sanity check
 701                         if (subset.size() != 0) {
 702                                 m->mothurOut("Your groupfile does not match your fasta file."); m->mothurOutEndLine();
 703                                 for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
 704                                         m->mothurOut("[ERROR]: " + *it + " is missing from your groupfile."); m->mothurOutEndLine();
 705                                 }
 706                         }
 707                 }
 708
 709                 return 0;
 710
 711         }
 712         catch(exception& e) {
 713                 m->errorOut(e, "SubSampleCommand", "getSubSampleFasta");
 714                 exit(1);
 715         }
 716 }
 717 //**********************************************************************************************************************
 718 int SubSampleCommand::getNames() {
 719         try {
 720
 721                 ifstream in;
 722                 m->openInputFile(fastafile, in);
 723
 724                 string thisname;
 725                 while(!in.eof()){
 726
 727                         if (m->control_pressed) { in.close(); return 0; }
 728
 729                         Sequence currSeq(in);
 730                         thisname = currSeq.getName();
 731
 732                         if (thisname != "") {
 733                                 vector<string> temp; temp.push_back(thisname);
 734                                 nameMap[thisname] = temp;
 735                                 names.push_back(thisname);
 736                         }
 737                         m->gobble(in);
 738                 }
 739                 in.close();
 740
 741                 return 0;
 742
 743         }
 744         catch(exception& e) {
 745                 m->errorOut(e, "SubSampleCommand", "getNames");
 746                 exit(1);
 747         }
 748 }
 749 //**********************************************************************************************************************
 750 int SubSampleCommand::readNames() {
 751         try {
 752
 753         nameMap.clear();
 754         m->readNames(namefile, nameMap);
 755
 756         //save names of all sequences
 757         map<string, vector<string> >::iterator it;
 758         for (it = nameMap.begin(); it != nameMap.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { names.push_back((it->second)[i]); } }
 759
 760                 return 0;
 761
 762         }
 763         catch(exception& e) {
 764                 m->errorOut(e, "SubSampleCommand", "readNames");
 765                 exit(1);
 766         }
 767 }
 768 //**********************************************************************************************************************
 769 int SubSampleCommand::getSubSampleShared() {
 770         try {
 771
 772                 InputData* input = new InputData(sharedfile, "sharedfile");
 773                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 774                 string lastLabel = lookup[0]->getLabel();
 775
 776                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 777                 set<string> processedLabels;
 778                 set<string> userLabels = labels;
 779
 780                 if (size == 0) { //user has not set size, set size = smallest samples size
 781                         size = lookup[0]->getNumSeqs();
 782                         for (int i = 1; i < lookup.size(); i++) {
 783                                 int thisSize = lookup[i]->getNumSeqs();
 784
 785                                 if (thisSize < size) {  size = thisSize;        }
 786                         }
 787                 }else {
 788                         m->clearGroups();
 789                         Groups.clear();
 790                         vector<SharedRAbundVector*> temp;
 791                         for (int i = 0; i < lookup.size(); i++) {
 792                                 if (lookup[i]->getNumSeqs() < size) {
 793                                         m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
 794                                         delete lookup[i];
 795                                 }else {
 796                                         Groups.push_back(lookup[i]->getGroup());
 797                                         temp.push_back(lookup[i]);
 798                                 }
 799                         }
 800                         lookup = temp;
 801                         m->setGroups(Groups);
 802                 }
 803
 804                 if (lookup.size() == 0) {  m->mothurOut("The size you selected is too large, skipping shared file."); m->mothurOutEndLine(); delete input; return 0; }
 805
 806                 m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
 807
 808                 //as long as you are not at the end of the file or done wih the lines you want
 809                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 810                         if (m->control_pressed) {  delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }  return 0;  }
 811
 812                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 813
 814                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 815
 816                                 processShared(lookup);
 817
 818                                 processedLabels.insert(lookup[0]->getLabel());
 819                                 userLabels.erase(lookup[0]->getLabel());
 820                         }
 821
 822                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 823                                 string saveLabel = lookup[0]->getLabel();
 824
 825                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 826
 827                                 lookup = input->getSharedRAbundVectors(lastLabel);
 828                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 829
 830                                 processShared(lookup);
 831
 832                                 processedLabels.insert(lookup[0]->getLabel());
 833                                 userLabels.erase(lookup[0]->getLabel());
 834
 835                                 //restore real lastlabel to save below
 836                                 lookup[0]->setLabel(saveLabel);
 837                         }
 838
 839                         lastLabel = lookup[0]->getLabel();
 840                         //prevent memory leak
 841                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 842
 843                         //get next line to process
 844                         lookup = input->getSharedRAbundVectors();
 845                 }
 846
 847
 848                 if (m->control_pressed) {   return 0;  }
 849
 850                 //output error messages about any remaining user labels
 851                 set<string>::iterator it;
 852                 bool needToRun = false;
 853                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 854                         m->mothurOut("Your file does not include the label " + *it);
 855                         if (processedLabels.count(lastLabel) != 1) {
 856                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 857                                 needToRun = true;
 858                         }else {
 859                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 860                         }
 861                 }
 862
 863                 //run last label if you need to
 864                 if (needToRun == true)  {
 865                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 866                         lookup = input->getSharedRAbundVectors(lastLabel);
 867
 868                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 869
 870                         processShared(lookup);
 871
 872                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 873                 }
 874
 875                 delete input;
 876
 877                 return 0;
 878
 879         }
 880         catch(exception& e) {
 881                 m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
 882                 exit(1);
 883         }
 884 }
 885 //**********************************************************************************************************************
 886 int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
 887         try {
 888
 889                 //save mothurOut's binLabels to restore for next label
 890                 vector<string> saveBinLabels = m->currentBinLabels;
 891
 892                 string thisOutputDir = outputDir;
 893                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 894                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + "." +getOutputFileNameTag("shared", sharedfile);
 895         SubSample sample;
 896         vector<string> subsampledLabels = sample.getSample(thislookup, size);
 897
 898         if (m->control_pressed) {  return 0; }
 899
 900         ofstream out;
 901                 m->openOutputFile(outputFileName, out);
 902                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 903
 904         m->currentBinLabels = subsampledLabels;
 905
 906                 thislookup[0]->printHeaders(out);
 907
 908                 for (int i = 0; i < thislookup.size(); i++) {
 909                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 910                         thislookup[i]->print(out);
 911                 }
 912                 out.close();
 913
 914
 915         //save mothurOut's binLabels to restore for next label
 916                 m->currentBinLabels = saveBinLabels;
 917
 918                 return 0;
 919
 920         }
 921         catch(exception& e) {
 922                 m->errorOut(e, "SubSampleCommand", "processShared");
 923                 exit(1);
 924         }
 925 }
 926 //**********************************************************************************************************************
 927 int SubSampleCommand::getSubSampleList() {
 928         try {
 929
 930                 string thisOutputDir = outputDir;
 931                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 932                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 933                 ofstream out;
 934                 m->openOutputFile(outputFileName, out);
 935                 outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 936
 937                 InputData* input = new InputData(listfile, "list");
 938                 ListVector* list = input->getListVector();
 939                 string lastLabel = list->getLabel();
 940
 941                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 942                 set<string> processedLabels;
 943                 set<string> userLabels = labels;
 944
 945                 ofstream outGroup;
 946                 GroupMap groupMap;
 947                 if (groupfile != "") {
 948                         groupMap.readMap(groupfile);
 949
 950                         //takes care of user setting groupNames that are invalid or setting groups=all
 951                         SharedUtil util; vector<string> namesGroups = groupMap.getNamesOfGroups(); util.setGroups(Groups, namesGroups);
 952
 953                         //create outputfiles
 954                         string groupOutputDir = outputDir;
 955                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
 956                         string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
 957                         m->openOutputFile(groupOutputFileName, outGroup);
 958                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
 959
 960                         //file mismatch quit
 961                         if (list->getNumSeqs() != groupMap.getNumSeqs()) {
 962                                 m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap.getNumSeqs()) + ", please correct.");
 963                                 m->mothurOutEndLine(); delete list; delete input; out.close(); outGroup.close(); return 0;
 964                         }
 965                 }else if (countfile != "") {
 966             if (ct.hasGroupInfo()) {
 967                 SharedUtil util;
 968                 vector<string> namesGroups = ct.getNamesOfGroups();
 969                 util.setGroups(Groups, namesGroups);
 970             }
 971
 972             //file mismatch quit
 973                         if (list->getNumSeqs() != ct.getNumUniqueSeqs()) {
 974                                 m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your count file contains " + toString(ct.getNumUniqueSeqs()) + " unique sequences, please correct.");
 975                                 m->mothurOutEndLine();
 976                                 return 0;
 977                         }
 978         }
 979
 980                 //make sure that if your picked groups size is not too big
 981                 if (persample) {
 982                         if (size == 0) { //user has not set size, set size = smallest samples size
 983                                 if (countfile == "") { size = groupMap.getNumSeqs(Groups[0]); }
 984                 else {  size = ct.getGroupCount(Groups[0]);  }
 985
 986                                 for (int i = 1; i < Groups.size(); i++) {
 987                                         int thisSize = 0;
 988                     if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
 989                     else {  thisSize = ct.getGroupCount(Groups[i]);  }
 990
 991                                         if (thisSize < size) {  size = thisSize;        }
 992                                 }
 993                         }else { //make sure size is not too large
 994                                 vector<string> newGroups;
 995                                 for (int i = 0; i < Groups.size(); i++) {
 996                                         int thisSize = 0;
 997                     if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
 998                     else {  thisSize = ct.getGroupCount(Groups[i]);  }
 999
1000                                         if (thisSize >= size) { newGroups.push_back(Groups[i]); }
1001                                         else {  m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
1002                                 }
1003                                 Groups = newGroups;
1004                 if (newGroups.size() == 0) {  m->mothurOut("[ERROR]: all groups removed."); m->mothurOutEndLine(); m->control_pressed = true; }
1005                         }
1006
1007                         m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
1008                 }else{
1009             if (pickedGroups) {
1010                                 int total = 0;
1011                                 for(int i = 0; i < Groups.size(); i++) {
1012                     if (countfile == "") { total += groupMap.getNumSeqs(Groups[i]); }
1013                     else {  total += ct.getGroupCount(Groups[i]);  }
1014                                 }
1015
1016                                 if (size == 0) { //user has not set size, set size = 10% samples size
1017                                         size = int (total * 0.10);
1018                                 }
1019
1020                                 if (total < size) {
1021                                         if (size != 0) {
1022                                                 m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
1023                                         }
1024                                         size = int (total * 0.10);
1025                                 }
1026
1027                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
1028                         }else {
1029                 if (size == 0) { //user has not set size, set size = 10% samples size
1030                                         if (countfile == "") {  size = int (list->getNumSeqs() * 0.10);  }
1031                     else { size = int (ct.getNumSeqs() * 0.10);  }
1032                                 }
1033
1034                                 int thisSize = 0;
1035                 if (countfile == "") { thisSize = list->getNumSeqs();  }
1036                 else { thisSize = ct.getNumSeqs(); }
1037
1038                                 if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
1039                                         size = thisSize;
1040                                 }
1041
1042                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine();
1043             }
1044         }
1045
1046         set<string> subset; //dont want repeat sequence names added
1047                 if (countfile == "") {
1048             //fill names
1049             for (int i = 0; i < list->getNumBins(); i++) {
1050                 string binnames = list->get(i);
1051                 vector<string> thisBin;
1052                 m->splitAtComma(binnames, thisBin);
1053
1054                 for(int j=0;j<thisBin.size();j++){
1055                     if (groupfile != "") { //if there is a groupfile given fill in group info
1056                         string group = groupMap.getGroup(thisBin[j]);
1057                         if (group == "not found") { m->mothurOut("[ERROR]: " + thisBin[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
1058
1059                                                 //if hte user picked groups, we only want to keep the names of sequences from those groups
1060                                                 if (pickedGroups) { if (m->inUsersGroups(group, Groups)) { names.push_back(thisBin[j]); }  }
1061                                                 else{ names.push_back(thisBin[j]); }
1062                     }//save everyone, group
1063                     else{ names.push_back(thisBin[j]); }
1064                 }
1065             }
1066
1067             random_shuffle(names.begin(), names.end());
1068
1069             //randomly select a subset of those names to include in the subsample
1070             if (persample) {
1071                 //initialize counts
1072                 map<string, int> groupCounts;
1073                 map<string, int>::iterator itGroupCounts;
1074                 for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
1075
1076                 for (int j = 0; j < names.size(); j++) {
1077
1078                     if (m->control_pressed) { delete list; delete input;  return 0; }
1079
1080                     string group = groupMap.getGroup(names[j]);
1081                     if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
1082                     else{
1083                         itGroupCounts = groupCounts.find(group);
1084                         if (itGroupCounts != groupCounts.end()) {
1085                             if (groupCounts[group] < size) {    subset.insert(names[j]);        groupCounts[group]++; }
1086                         }
1087                     }
1088                 }
1089             }else{
1090                 for (int j = 0; j < size; j++) {
1091                     if (m->control_pressed) { break; }
1092                     subset.insert(names[j]);
1093                 }
1094             }
1095
1096             if (groupfile != "") {
1097                 //write out new groupfile
1098                 for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
1099                     string group = groupMap.getGroup(*it);
1100                     if (group == "not found") { group = "NOTFOUND"; }
1101                     outGroup << *it << '\t' << group << endl;
1102                 }
1103                 outGroup.close();
1104             }
1105                 }else {
1106             SubSample sample; CountTable sampledCt;
1107
1108             if (persample)  { sampledCt = sample.getSample(ct, size, Groups);               }
1109             else            { sampledCt = sample.getSample(ct, size, Groups, pickedGroups); }
1110
1111             vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
1112             for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
1113
1114             string countOutputDir = outputDir;
1115             if (outputDir == "") {  countOutputDir += m->hasPath(countfile);  }
1116             string countOutputFileName = countOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
1117             outputTypes["count"].push_back(countOutputFileName);  outputNames.push_back(countOutputFileName);
1118             sampledCt.printTable(countOutputFileName);
1119         }
1120
1121                 //as long as you are not at the end of the file or done wih the lines you want
1122                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1123
1124                         if (m->control_pressed) {  delete list; delete input;  out.close();  return 0;  }
1125
1126                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
1127
1128                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1129
1130                                 processList(list, out, subset);
1131
1132                                 processedLabels.insert(list->getLabel());
1133                                 userLabels.erase(list->getLabel());
1134                         }
1135
1136                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1137                                 string saveLabel = list->getLabel();
1138
1139                                 delete list;
1140
1141                                 list = input->getListVector(lastLabel);
1142                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1143
1144                                 processList(list, out, subset);
1145
1146                                 processedLabels.insert(list->getLabel());
1147                                 userLabels.erase(list->getLabel());
1148
1149                                 //restore real lastlabel to save below
1150                                 list->setLabel(saveLabel);
1151                         }
1152
1153                         lastLabel = list->getLabel();
1154
1155                         delete list; list = NULL;
1156
1157                         //get next line to process
1158                         list = input->getListVector();
1159                 }
1160
1161
1162                 if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); return 0;  }
1163
1164                 //output error messages about any remaining user labels
1165                 set<string>::iterator it;
1166                 bool needToRun = false;
1167                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1168                         m->mothurOut("Your file does not include the label " + *it);
1169                         if (processedLabels.count(lastLabel) != 1) {
1170                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1171                                 needToRun = true;
1172                         }else {
1173                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1174                         }
1175                 }
1176
1177                 //run last label if you need to
1178                 if (needToRun == true)  {
1179                         if (list != NULL) { delete list; }
1180
1181                         list = input->getListVector(lastLabel);
1182
1183                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1184
1185                         processList(list, out, subset);
1186
1187                         delete list; list = NULL;
1188                 }
1189
1190                 out.close();
1191                 if (list != NULL) { delete list; }
1192                 delete input;
1193
1194                 return 0;
1195
1196         }
1197         catch(exception& e) {
1198                 m->errorOut(e, "SubSampleCommand", "getSubSampleList");
1199                 exit(1);
1200         }
1201 }
1202 //**********************************************************************************************************************
1203 int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>& subset) {
1204         try {
1205
1206                 int numBins = list->getNumBins();
1207
1208                 ListVector* temp = new ListVector();
1209                 temp->setLabel(list->getLabel());
1210
1211                 for (int i = 0; i < numBins; i++) {
1212
1213                         if (m->control_pressed) { break; }
1214
1215                         string bin = list->get(i);
1216             vector<string> binnames;
1217             m->splitAtComma(bin, binnames);
1218
1219             string newNames = "";
1220                         for(int j=0;j<binnames.size();j++){ if (subset.count(binnames[j]) != 0) {  newNames += binnames[j] + ",";  } }
1221
1222                         //if there are names in this bin add to new list
1223                         if (newNames != "") {
1224                                 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
1225                                 temp->push_back(newNames);
1226                         }
1227                 }
1228
1229                 delete list;
1230                 list = temp;
1231
1232                 if (m->control_pressed) { return 0; }
1233
1234                 list->print(out);
1235
1236                 return 0;
1237
1238         }
1239         catch(exception& e) {
1240                 m->errorOut(e, "SubSampleCommand", "processList");
1241                 exit(1);
1242         }
1243 }
1244 //**********************************************************************************************************************
1245 int SubSampleCommand::getSubSampleRabund() {
1246         try {
1247                 InputData* input = new InputData(rabundfile, "rabund");
1248                 RAbundVector* rabund = input->getRAbundVector();
1249                 string lastLabel = rabund->getLabel();
1250
1251                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1252                 set<string> processedLabels;
1253                 set<string> userLabels = labels;
1254
1255                 if (size == 0) { //user has not set size, set size = 10%
1256                         size = int((rabund->getNumSeqs()) * 0.10);
1257                 }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; }
1258
1259                 m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1260
1261                 string thisOutputDir = outputDir;
1262                 if (outputDir == "") {  thisOutputDir += m->hasPath(rabundfile);  }
1263                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile);
1264                 ofstream out;
1265                 m->openOutputFile(outputFileName, out);
1266                 outputTypes["rabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1267
1268                 //as long as you are not at the end of the file or done wih the lines you want
1269                 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1270                         if (m->control_pressed) {  delete input; delete rabund; out.close(); return 0;  }
1271
1272                         if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
1273
1274                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1275
1276                                 processRabund(rabund, out);
1277
1278                                 processedLabels.insert(rabund->getLabel());
1279                                 userLabels.erase(rabund->getLabel());
1280                         }
1281
1282                         if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1283                                 string saveLabel = rabund->getLabel();
1284
1285                                 delete rabund;
1286
1287                                 rabund = input->getRAbundVector(lastLabel);
1288                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1289
1290                                 processRabund(rabund, out);
1291
1292                                 processedLabels.insert(rabund->getLabel());
1293                                 userLabels.erase(rabund->getLabel());
1294
1295                                 //restore real lastlabel to save below
1296                                 rabund->setLabel(saveLabel);
1297                         }
1298
1299                         lastLabel = rabund->getLabel();
1300
1301                         //prevent memory leak
1302                         delete rabund; rabund = NULL;
1303
1304                         //get next line to process
1305                         rabund = input->getRAbundVector();
1306                 }
1307
1308
1309                 if (m->control_pressed) {  out.close(); return 0;  }
1310
1311                 //output error messages about any remaining user labels
1312                 set<string>::iterator it;
1313                 bool needToRun = false;
1314                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1315                         m->mothurOut("Your file does not include the label " + *it);
1316                         if (processedLabels.count(lastLabel) != 1) {
1317                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1318                                 needToRun = true;
1319                         }else {
1320                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1321                         }
1322                 }
1323
1324                 //run last label if you need to
1325                 if (needToRun == true)  {
1326                         if (rabund != NULL) { delete rabund; }
1327
1328                         rabund = input->getRAbundVector(lastLabel);
1329
1330                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1331
1332                         processRabund(rabund, out);
1333
1334                         delete rabund;
1335                 }
1336
1337                 delete input;
1338                 out.close();
1339
1340                 return 0;
1341
1342         }
1343         catch(exception& e) {
1344                 m->errorOut(e, "SubSampleCommand", "getSubSampleRabund");
1345                 exit(1);
1346         }
1347 }
1348 //**********************************************************************************************************************
1349 int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) {
1350         try {
1351
1352                 int numBins = rabund->getNumBins();
1353                 int thisSize = rabund->getNumSeqs();
1354
1355                 if (thisSize != size) {
1356
1357                         OrderVector* order = new OrderVector();
1358                         for(int p=0;p<numBins;p++){
1359                                 for(int j=0;j<rabund->get(p);j++){
1360                                         order->push_back(p);
1361                                 }
1362                         }
1363                         random_shuffle(order->begin(), order->end());
1364
1365                         RAbundVector* temp = new RAbundVector(numBins);
1366                         temp->setLabel(rabund->getLabel());
1367
1368                         delete rabund;
1369                         rabund = temp;
1370
1371                         for (int j = 0; j < size; j++) {
1372
1373                                 if (m->control_pressed) { delete order; return 0; }
1374
1375                                 int bin = order->get(j);
1376
1377                                 int abund = rabund->get(bin);
1378                                 rabund->set(bin, (abund+1));
1379                         }
1380
1381                         delete order;
1382                 }
1383
1384                 if (m->control_pressed) { return 0; }
1385
1386                 rabund->print(out);
1387
1388                 return 0;
1389
1390         }
1391         catch(exception& e) {
1392                 m->errorOut(e, "SubSampleCommand", "processRabund");
1393                 exit(1);
1394         }
1395 }
1396 //**********************************************************************************************************************
1397 int SubSampleCommand::getSubSampleSabund() {
1398         try {
1399
1400                 InputData* input = new InputData(sabundfile, "sabund");
1401                 SAbundVector* sabund = input->getSAbundVector();
1402                 string lastLabel = sabund->getLabel();
1403
1404                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1405                 set<string> processedLabels;
1406                 set<string> userLabels = labels;
1407
1408                 if (size == 0) { //user has not set size, set size = 10%
1409                         size = int((sabund->getNumSeqs()) * 0.10);
1410                 }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; }
1411
1412
1413                 m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1414
1415                 string thisOutputDir = outputDir;
1416                 if (outputDir == "") {  thisOutputDir += m->hasPath(sabundfile);  }
1417                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile);
1418                 ofstream out;
1419                 m->openOutputFile(outputFileName, out);
1420                 outputTypes["sabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1421
1422
1423                 //as long as you are not at the end of the file or done wih the lines you want
1424                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1425                         if (m->control_pressed) {  delete input; delete sabund; out.close(); return 0;  }
1426
1427                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
1428
1429                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1430
1431                                 processSabund(sabund, out);
1432
1433                                 processedLabels.insert(sabund->getLabel());
1434                                 userLabels.erase(sabund->getLabel());
1435                         }
1436
1437                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1438                                 string saveLabel = sabund->getLabel();
1439
1440                                 delete sabund;
1441
1442                                 sabund = input->getSAbundVector(lastLabel);
1443                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1444
1445                                 processSabund(sabund, out);
1446
1447                                 processedLabels.insert(sabund->getLabel());
1448                                 userLabels.erase(sabund->getLabel());
1449
1450                                 //restore real lastlabel to save below
1451                                 sabund->setLabel(saveLabel);
1452                         }
1453
1454                         lastLabel = sabund->getLabel();
1455
1456                         //prevent memory leak
1457                         delete sabund; sabund = NULL;
1458
1459                         //get next line to process
1460                         sabund = input->getSAbundVector();
1461                 }
1462
1463
1464                 if (m->control_pressed) {  out.close(); return 0;  }
1465
1466                 //output error messages about any remaining user labels
1467                 set<string>::iterator it;
1468                 bool needToRun = false;
1469                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1470                         m->mothurOut("Your file does not include the label " + *it);
1471                         if (processedLabels.count(lastLabel) != 1) {
1472                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1473                                 needToRun = true;
1474                         }else {
1475                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1476                         }
1477                 }
1478
1479                 //run last label if you need to
1480                 if (needToRun == true)  {
1481                         if (sabund != NULL) { delete sabund; }
1482
1483                         sabund = input->getSAbundVector(lastLabel);
1484
1485                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1486
1487                         processSabund(sabund, out);
1488
1489                         delete sabund;
1490                 }
1491
1492                 delete input;
1493                 out.close();
1494
1495                 return 0;
1496
1497         }
1498         catch(exception& e) {
1499                 m->errorOut(e, "SubSampleCommand", "getSubSampleSabund");
1500                 exit(1);
1501         }
1502 }
1503 //**********************************************************************************************************************
1504 int SubSampleCommand::processSabund(SAbundVector*& sabund, ofstream& out) {
1505         try {
1506
1507                 RAbundVector* rabund = new RAbundVector();
1508                 *rabund = sabund->getRAbundVector();
1509
1510                 int numBins = rabund->getNumBins();
1511                 int thisSize = rabund->getNumSeqs();
1512
1513                 if (thisSize != size) {
1514
1515                         OrderVector* order = new OrderVector();
1516                         for(int p=0;p<numBins;p++){
1517                                 for(int j=0;j<rabund->get(p);j++){
1518                                         order->push_back(p);
1519                                 }
1520                         }
1521                         random_shuffle(order->begin(), order->end());
1522
1523                         RAbundVector* temp = new RAbundVector(numBins);
1524                         temp->setLabel(rabund->getLabel());
1525
1526                         delete rabund;
1527                         rabund = temp;
1528
1529                         for (int j = 0; j < size; j++) {
1530
1531                                 if (m->control_pressed) { delete order; return 0; }
1532
1533                                 int bin = order->get(j);
1534
1535                                 int abund = rabund->get(bin);
1536                                 rabund->set(bin, (abund+1));
1537                         }
1538
1539                         delete order;
1540                 }
1541
1542                 if (m->control_pressed) { return 0; }
1543
1544                 delete sabund;
1545                 sabund = new SAbundVector();
1546                 *sabund = rabund->getSAbundVector();
1547                 delete rabund;
1548
1549                 sabund->print(out);
1550
1551                 return 0;
1552
1553         }
1554         catch(exception& e) {
1555                 m->errorOut(e, "SubSampleCommand", "processSabund");
1556                 exit(1);
1557         }
1558 }
1559 //**********************************************************************************************************************
1560
1561
1562