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 "getseqscommand.h"
  14 #include "subsample.h"
  15
  16 //**********************************************************************************************************************
  17 vector<string> SubSampleCommand::setParameters(){
  18         try {
  19                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none","fasta",false,false,true); parameters.push_back(pfasta);
  20         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
  21         CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
  22         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
  23                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
  24                 CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none","list",false,false,true); parameters.push_back(plist);
  25                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none","shared",false,false,true); parameters.push_back(pshared);
  26                 CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none","rabund",false,false); parameters.push_back(prabund);
  27                 CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none","sabund",false,false); parameters.push_back(psabund);
  28                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  29                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  30                 CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(psize);
  31                 CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(ppersample);
  32                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  33                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  34
  35                 vector<string> myArray;
  36                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  37                 return myArray;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "SubSampleCommand", "setParameters");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 string SubSampleCommand::getHelpString(){
  46         try {
  47                 string helpString = "";
  48                 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";
  49                 helpString += "The sub.sample command parameters are fasta, name, list, group, count, rabund, sabund, shared, taxonomy, groups, size, persample and label.  You must provide a fasta, list, sabund, rabund or shared file as an input file.\n";
  50                 helpString += "The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n";
  51                 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";
  52                 helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
  53                 helpString += "The size parameter allows you indicate the size of your subsample.\n";
  54                 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";
  55                 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";
  56                 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";
  57                 helpString += "The sub.sample command should be in the following format: sub.sample(list=yourListFile, group=yourGroupFile, groups=yourGroups, label=yourLabels).\n";
  58                 helpString += "Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n";
  59                 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
  60                 helpString += "The sub.sample command outputs a .subsample file.\n";
  61                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  62                 return helpString;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "SubSampleCommand", "getHelpString");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70 string SubSampleCommand::getOutputPattern(string type) {
  71     try {
  72         string pattern = "";
  73
  74         if (type == "fasta")            {   pattern = "[filename],subsample,[extension]";    }
  75         else if (type == "sabund")      {   pattern = "[filename],subsample,[extension]";    }
  76         else if (type == "name")        {   pattern = "[filename],subsample,[extension]";    }
  77         else if (type == "group")       {   pattern = "[filename],subsample,[extension]";    }
  78         else if (type == "count")       {   pattern = "[filename],subsample,[extension]";    }
  79         else if (type == "list")        {   pattern = "[filename],subsample,[extension]";    }
  80         else if (type == "taxonomy")    {   pattern = "[filename],subsample,[extension]";    }
  81         else if (type == "shared")      {   pattern = "[filename],[distance],subsample,[extension]";    }
  82         else if (type == "rabund")      {   pattern = "[filename],subsample,[extension]";    }
  83         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  84
  85         return pattern;
  86     }
  87     catch(exception& e) {
  88         m->errorOut(e, "SubSampleCommand", "getOutputPattern");
  89         exit(1);
  90     }
  91 }
  92 //**********************************************************************************************************************
  93 SubSampleCommand::SubSampleCommand(){
  94         try {
  95                 abort = true; calledHelp = true;
  96                 setParameters();
  97                 vector<string> tempOutNames;
  98                 outputTypes["shared"] = tempOutNames;
  99                 outputTypes["list"] = tempOutNames;
 100                 outputTypes["rabund"] = tempOutNames;
 101                 outputTypes["sabund"] = tempOutNames;
 102                 outputTypes["fasta"] = tempOutNames;
 103                 outputTypes["name"] = tempOutNames;
 104                 outputTypes["group"] = tempOutNames;
 105         outputTypes["count"] = tempOutNames;
 106         outputTypes["taxonomy"] = tempOutNames;
 107         }
 108         catch(exception& e) {
 109                 m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
 110                 exit(1);
 111         }
 112 }
 113 //**********************************************************************************************************************
 114 SubSampleCommand::SubSampleCommand(string option) {
 115         try {
 116                 abort = false; calledHelp = false;
 117                 allLines = 1;
 118
 119                 //allow user to run help
 120                 if(option == "help") { help(); abort = true; calledHelp = true; }
 121                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 122
 123                 else {
 124                         vector<string> myArray = setParameters();
 125
 126                         OptionParser parser(option);
 127                         map<string,string> parameters = parser.getParameters();
 128
 129                         ValidParameters validParameter;
 130
 131                         //check to make sure all parameters are valid for command
 132                         map<string,string>::iterator it;
 133                         for (it = parameters.begin(); it != parameters.end(); it++) {
 134                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 135                         }
 136
 137                         //initialize outputTypes
 138                         vector<string> tempOutNames;
 139                         outputTypes["shared"] = tempOutNames;
 140                         outputTypes["list"] = tempOutNames;
 141                         outputTypes["rabund"] = tempOutNames;
 142                         outputTypes["sabund"] = tempOutNames;
 143                         outputTypes["fasta"] = tempOutNames;
 144                         outputTypes["name"] = tempOutNames;
 145                         outputTypes["group"] = tempOutNames;
 146             outputTypes["count"] = tempOutNames;
 147             outputTypes["taxonomy"] = tempOutNames;
 148
 149                         //if the user changes the output directory command factory will send this info to us in the output parameter
 150                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 151
 152                         //if the user changes the input directory command factory will send this info to us in the output parameter
 153                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 154                         if (inputDir == "not found"){   inputDir = "";          }
 155                         else {
 156                                 string path;
 157                                 it = parameters.find("list");
 158                                 //user has given a template file
 159                                 if(it != parameters.end()){
 160                                         path = m->hasPath(it->second);
 161                                         //if the user has not given a path then, add inputdir. else leave path alone.
 162                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 163                                 }
 164
 165                                 it = parameters.find("fasta");
 166                                 //user has given a template file
 167                                 if(it != parameters.end()){
 168                                         path = m->hasPath(it->second);
 169                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 171                                 }
 172
 173                                 it = parameters.find("shared");
 174                                 //user has given a template file
 175                                 if(it != parameters.end()){
 176                                         path = m->hasPath(it->second);
 177                                         //if the user has not given a path then, add inputdir. else leave path alone.
 178                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 179                                 }
 180
 181                                 it = parameters.find("group");
 182                                 //user has given a template file
 183                                 if(it != parameters.end()){
 184                                         path = m->hasPath(it->second);
 185                                         //if the user has not given a path then, add inputdir. else leave path alone.
 186                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 187                                 }
 188
 189                                 it = parameters.find("sabund");
 190                                 //user has given a template file
 191                                 if(it != parameters.end()){
 192                                         path = m->hasPath(it->second);
 193                                         //if the user has not given a path then, add inputdir. else leave path alone.
 194                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 195                                 }
 196
 197                                 it = parameters.find("rabund");
 198                                 //user has given a template file
 199                                 if(it != parameters.end()){
 200                                         path = m->hasPath(it->second);
 201                                         //if the user has not given a path then, add inputdir. else leave path alone.
 202                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 203                                 }
 204
 205                                 it = parameters.find("name");
 206                                 //user has given a template file
 207                                 if(it != parameters.end()){
 208                                         path = m->hasPath(it->second);
 209                                         //if the user has not given a path then, add inputdir. else leave path alone.
 210                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 211                                 }
 212
 213                 it = parameters.find("count");
 214                                 //user has given a template file
 215                                 if(it != parameters.end()){
 216                                         path = m->hasPath(it->second);
 217                                         //if the user has not given a path then, add inputdir. else leave path alone.
 218                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 219                                 }
 220
 221                 it = parameters.find("taxonomy");
 222                                 //user has given a template file
 223                                 if(it != parameters.end()){
 224                                         path = m->hasPath(it->second);
 225                                         //if the user has not given a path then, add inputdir. else leave path alone.
 226                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 227                                 }
 228                         }
 229
 230                         //check for required parameters
 231                         listfile = validParameter.validFile(parameters, "list", true);
 232                         if (listfile == "not open") { listfile = ""; abort = true; }
 233                         else if (listfile == "not found") { listfile = ""; }
 234                         else { m->setListFile(listfile); }
 235
 236                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 237                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 238                         else if (sabundfile == "not found") { sabundfile = ""; }
 239                         else { m->setSabundFile(sabundfile); }
 240
 241                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 242                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 243                         else if (rabundfile == "not found") { rabundfile = ""; }
 244                         else { m->setRabundFile(rabundfile); }
 245
 246                         fastafile = validParameter.validFile(parameters, "fasta", true);
 247                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 248                         else if (fastafile == "not found") { fastafile = ""; }
 249                         else { m->setFastaFile(fastafile); }
 250
 251                         sharedfile = validParameter.validFile(parameters, "shared", true);
 252                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 253                         else if (sharedfile == "not found") { sharedfile = ""; }
 254                         else { m->setSharedFile(sharedfile); }
 255
 256                         namefile = validParameter.validFile(parameters, "name", true);
 257                         if (namefile == "not open") { namefile = ""; abort = true; }
 258                         else if (namefile == "not found") { namefile = ""; }
 259                         else { m->setNameFile(namefile); }
 260
 261                         groupfile = validParameter.validFile(parameters, "group", true);
 262                         if (groupfile == "not open") { groupfile = ""; abort = true; }
 263                         else if (groupfile == "not found") { groupfile = ""; }
 264                         else { m->setGroupFile(groupfile); }
 265
 266             taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
 267                         if (taxonomyfile == "not open") { taxonomyfile = ""; abort = true; }
 268                         else if (taxonomyfile == "not found") { taxonomyfile = ""; }
 269                         else { m->setTaxonomyFile(taxonomyfile); }
 270
 271             countfile = validParameter.validFile(parameters, "count", true);
 272                         if (countfile == "not open") { countfile = ""; abort = true; }
 273                         else if (countfile == "not found") { countfile = "";  }
 274                         else {
 275                 m->setCountTableFile(countfile);
 276                 ct.readTable(countfile, true, false);
 277             }
 278
 279             if ((namefile != "") && (countfile != "")) {
 280                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 281             }
 282
 283             if ((groupfile != "") && (countfile != "")) {
 284                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 285             }
 286
 287                         //check for optional parameter and set defaults
 288                         // ...at some point should added some additional type checking...
 289                         label = validParameter.validFile(parameters, "label", false);
 290                         if (label == "not found") { label = ""; }
 291                         else {
 292                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 293                                 else { allLines = 1;  }
 294                         }
 295
 296                         groups = validParameter.validFile(parameters, "groups", false);
 297                         if (groups == "not found") { groups = ""; pickedGroups = false; }
 298                         else {
 299                                 pickedGroups = true;
 300                                 m->splitAtDash(groups, Groups);
 301                                 m->setGroups(Groups);
 302                         }
 303
 304                         string temp = validParameter.validFile(parameters, "size", false);              if (temp == "not found"){       temp = "0";             }
 305                         m->mothurConvert(temp, size);
 306
 307                         temp = validParameter.validFile(parameters, "persample", false);                if (temp == "not found"){       temp = "f";             }
 308                         persample = m->isTrue(temp);
 309
 310                         if ((groupfile == "") && (countfile == "")) { persample = false; }
 311             if (countfile != "") {
 312                 if (!ct.hasGroupInfo()) {
 313                     persample = false;
 314                     if (pickedGroups) { m->mothurOut("You cannot pick groups without group info in your count file."); m->mothurOutEndLine(); abort = true; }
 315                 }
 316             }
 317
 318                         if ((namefile != "") && ((fastafile == "") && (taxonomyfile == ""))) { m->mothurOut("You may only use a name file with a fasta file or taxonomy file."); m->mothurOutEndLine(); abort = true; }
 319
 320             if ((taxonomyfile != "") && ((fastafile == "") && (listfile == ""))) { m->mothurOut("You may only use a taxonomyfile with a fastafile or listfile."); m->mothurOutEndLine(); abort = true; }
 321
 322
 323                         if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) {
 324                                 m->mothurOut("You must provide a fasta, list, sabund, rabund or shared file as an input file."); m->mothurOutEndLine(); abort = true; }
 325
 326                         if (pickedGroups && ((groupfile == "") && (sharedfile == "") && (countfile == ""))) {
 327                                 m->mothurOut("You cannot pick groups without a valid group, count or shared file."); m->mothurOutEndLine(); abort = true; }
 328
 329                         if (((groupfile != "") || (countfile != "")) && ((fastafile == "") && (listfile == ""))) {
 330                                 m->mothurOut("Group or count files are only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
 331
 332                         if (((groupfile != "") || (countfile != "")) && ((fastafile != "") && (listfile != ""))) {
 333                                 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; }
 334
 335             if (countfile == "") {
 336                 if ((fastafile != "") && (namefile == "")) {
 337                     vector<string> files; files.push_back(fastafile);
 338                     parser.getNameFile(files);
 339                 }
 340             }
 341                 }
 342
 343         }
 344         catch(exception& e) {
 345                 m->errorOut(e, "SubSampleCommand", "SubSampleCommand");
 346                 exit(1);
 347         }
 348 }
 349 //**********************************************************************************************************************
 350
 351 int SubSampleCommand::execute(){
 352         try {
 353
 354                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 355
 356                 if (sharedfile != "")   {   getSubSampleShared();       }
 357                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 358
 359                 if (listfile != "")             {   getSubSampleList();         }
 360                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 361
 362                 if (rabundfile != "")   {   getSubSampleRabund();       }
 363                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 364
 365                 if (sabundfile != "")   {   getSubSampleSabund();       }
 366                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 367
 368                 if (fastafile != "")    {   getSubSampleFasta();        }
 369                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); return 0; } }
 370
 371                 //set fasta file as new current fastafile
 372                 string current = "";
 373                 itTypes = outputTypes.find("fasta");
 374                 if (itTypes != outputTypes.end()) {
 375                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 376                 }
 377
 378                 itTypes = outputTypes.find("name");
 379                 if (itTypes != outputTypes.end()) {
 380                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 381                 }
 382
 383                 itTypes = outputTypes.find("group");
 384                 if (itTypes != outputTypes.end()) {
 385                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 386                 }
 387
 388                 itTypes = outputTypes.find("list");
 389                 if (itTypes != outputTypes.end()) {
 390                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 391                 }
 392
 393                 itTypes = outputTypes.find("shared");
 394                 if (itTypes != outputTypes.end()) {
 395                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
 396                 }
 397
 398                 itTypes = outputTypes.find("rabund");
 399                 if (itTypes != outputTypes.end()) {
 400                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 401                 }
 402
 403                 itTypes = outputTypes.find("sabund");
 404                 if (itTypes != outputTypes.end()) {
 405                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 406                 }
 407
 408         itTypes = outputTypes.find("count");
 409                 if (itTypes != outputTypes.end()) {
 410                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 411                 }
 412
 413         itTypes = outputTypes.find("taxonomy");
 414                 if (itTypes != outputTypes.end()) {
 415                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 416                 }
 417
 418                 m->mothurOutEndLine();
 419                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 420                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 421                 m->mothurOutEndLine();
 422
 423                 return 0;
 424         }
 425         catch(exception& e) {
 426                 m->errorOut(e, "SubSampleCommand", "execute");
 427                 exit(1);
 428         }
 429 }
 430 //**********************************************************************************************************************
 431 int SubSampleCommand::getSubSampleFasta() {
 432         try {
 433
 434                 if (namefile != "") { readNames(); }    //fills names with all names in namefile.
 435                 else { getNames(); }//no name file, so get list of names to pick from
 436
 437                 GroupMap groupMap;
 438                 if (groupfile != "") {
 439                         groupMap.readMap(groupfile);
 440
 441                         //takes care of user setting groupNames that are invalid or setting groups=all
 442                         SharedUtil util;
 443                         vector<string> namesGroups = groupMap.getNamesOfGroups();
 444                         util.setGroups(Groups, namesGroups);
 445
 446                         //file mismatch quit
 447                         if (names.size() != groupMap.getNumSeqs()) {
 448                                 m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap.getNumSeqs()) + ", please correct.");
 449                                 m->mothurOutEndLine();
 450                                 return 0;
 451                         }
 452                 }else if (countfile != "") {
 453             if (ct.hasGroupInfo()) {
 454                 SharedUtil util;
 455                 vector<string> namesGroups = ct.getNamesOfGroups();
 456                 util.setGroups(Groups, namesGroups);
 457             }
 458
 459             //file mismatch quit
 460                         if (names.size() != ct.getNumUniqueSeqs()) {
 461                                 m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your count file contains " + toString(ct.getNumUniqueSeqs()) + " unique sequences, please correct.");
 462                                 m->mothurOutEndLine();
 463                                 return 0;
 464                         }
 465         }
 466
 467                 if (m->control_pressed) { return 0; }
 468
 469                 //make sure that if your picked groups size is not too big
 470                 int thisSize = 0;
 471         if (countfile == "") { thisSize = names.size();  }
 472         else {  thisSize = ct. getNumSeqs();  }  //all seqs not just unique
 473
 474                 if (persample) {
 475                         if (size == 0) { //user has not set size, set size = smallest samples size
 476                                 if (countfile == "") { size = groupMap.getNumSeqs(Groups[0]); }
 477                 else {  size = ct.getGroupCount(Groups[0]);  }
 478
 479                                 for (int i = 1; i < Groups.size(); i++) {
 480                                         int thisSize = 0;
 481                     if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
 482                     else {  thisSize = ct.getGroupCount(Groups[i]);  }
 483
 484                                         if (thisSize < size) {  size = thisSize;        }
 485                                 }
 486                         }else { //make sure size is not too large
 487                                 vector<string> newGroups;
 488                                 for (int i = 0; i < Groups.size(); i++) {
 489                                         int thisSize = 0;
 490                     if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
 491                     else {  thisSize = ct.getGroupCount(Groups[i]);  }
 492
 493                                         if (thisSize >= size) { newGroups.push_back(Groups[i]); }
 494                                         else {  m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
 495                                 }
 496                                 Groups = newGroups;
 497                 if (newGroups.size() == 0) {  m->mothurOut("[ERROR]: all groups removed."); m->mothurOutEndLine(); m->control_pressed = true; }
 498                         }
 499
 500                         m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
 501                 }else {
 502                         if (pickedGroups) {
 503                                 int total = 0;
 504                                 for(int i = 0; i < Groups.size(); i++) {
 505                     if (countfile == "") { total += groupMap.getNumSeqs(Groups[i]); }
 506                     else {  total += ct.getGroupCount(Groups[i]);  }
 507                                 }
 508
 509                                 if (size == 0) { //user has not set size, set size = 10% samples size
 510                                         size = int (total * 0.10);
 511                                 }
 512
 513                                 if (total < size) {
 514                                         if (size != 0) {
 515                                                 m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
 516                                         }
 517                                         size = int (total * 0.10);
 518                                 }
 519
 520                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
 521                         }
 522
 523                         if (size == 0) { //user has not set size, set size = 10% samples size
 524                                 if (countfile == "") {  size = int (names.size() * 0.10); }
 525                 else {  size = int (ct.getNumSeqs() * 0.10); }
 526                         }
 527
 528
 529             if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
 530                     size = thisSize;
 531             }
 532
 533             if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); }
 534
 535                 }
 536                 random_shuffle(names.begin(), names.end());
 537
 538                 set<string> subset; //dont want repeat sequence names added
 539                 if (persample) {
 540             if (countfile == "") {
 541                 //initialize counts
 542                 map<string, int> groupCounts;
 543                 map<string, int>::iterator itGroupCounts;
 544                 for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
 545
 546                 for (int j = 0; j < names.size(); j++) {
 547
 548                     if (m->control_pressed) { return 0; }
 549
 550                     string group = groupMap.getGroup(names[j]);
 551                     if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 552                     else{
 553                         itGroupCounts = groupCounts.find(group);
 554                         if (itGroupCounts != groupCounts.end()) {
 555                             if (itGroupCounts->second < size) { subset.insert(names[j]);        (itGroupCounts->second)++; }
 556                         }
 557                     }
 558                 }
 559             }else {
 560                 SubSample sample;
 561                 CountTable sampledCt = sample.getSample(ct, size, Groups);
 562                 vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
 563                 for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
 564
 565                 string countOutputDir = outputDir;
 566                 if (outputDir == "") {  countOutputDir += m->hasPath(countfile);  }
 567                 map<string, string> variables;
 568                 variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
 569                 variables["[extension]"] = m->getExtension(countfile);
 570                 string countOutputFileName = getOutputFileName("count", variables);
 571                 outputTypes["count"].push_back(countOutputFileName);  outputNames.push_back(countOutputFileName);
 572                 sampledCt.printTable(countOutputFileName);
 573             }
 574                 }else {
 575                         if (countfile == "") {
 576                 //randomly select a subset of those names to include in the subsample
 577                 //since names was randomly shuffled just grab the next one
 578                 for (int j = 0; j < names.size(); j++) {
 579
 580                     if (m->control_pressed) { return 0; }
 581
 582                     if (groupfile != "") { //if there is a groupfile given fill in group info
 583                         string group = groupMap.getGroup(names[j]);
 584                         if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 585
 586                         if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
 587                             if (m->inUsersGroups(group, Groups)) {  subset.insert(names[j]); }
 588                         }else{  subset.insert(names[j]); }
 589                     }else{ //save everyone, group
 590                         subset.insert(names[j]);
 591                     }
 592
 593                     //do we have enough??
 594                     if (subset.size() == size) { break; }
 595                 }
 596             }else {
 597                 SubSample sample;
 598                 CountTable sampledCt = sample.getSample(ct, size, Groups, pickedGroups);
 599                 vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
 600                 for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
 601
 602                 string countOutputDir = outputDir;
 603                 if (outputDir == "") {  countOutputDir += m->hasPath(countfile);  }
 604                 map<string, string> variables;
 605                 variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
 606                 variables["[extension]"] = m->getExtension(countfile);
 607                 string countOutputFileName = getOutputFileName("count", variables);
 608                 outputTypes["count"].push_back(countOutputFileName);  outputNames.push_back(countOutputFileName);
 609                 sampledCt.printTable(countOutputFileName);
 610             }
 611                 }
 612
 613                 if (subset.size() == 0) {  m->mothurOut("The size you selected is too large, skipping fasta file."); m->mothurOutEndLine();  return 0; }
 614
 615                 string thisOutputDir = outputDir;
 616                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 617         map<string, string> variables;
 618         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
 619         variables["[extension]"] = m->getExtension(fastafile);
 620                 string outputFileName = getOutputFileName("fasta", variables);
 621                 ofstream out;
 622                 m->openOutputFile(outputFileName, out);
 623
 624                 //read through fasta file outputting only the names on the subsample list
 625                 ifstream in;
 626                 m->openInputFile(fastafile, in);
 627
 628                 string thisname;
 629                 int count = 0;
 630                 map<string, vector<string> >::iterator itNameMap;
 631
 632                 while(!in.eof()){
 633
 634                         if (m->control_pressed) { in.close(); out.close();  return 0; }
 635
 636                         Sequence currSeq(in);
 637                         thisname = currSeq.getName();
 638
 639                         if (thisname != "") {
 640
 641                                 //does the subset contain a sequence that this sequence represents
 642                                 itNameMap = nameMap.find(thisname);
 643                                 if (itNameMap != nameMap.end()) {
 644                                         vector<string> nameRepresents = itNameMap->second;
 645
 646                                         for (int i = 0; i < nameRepresents.size(); i++){
 647                                                 if (subset.count(nameRepresents[i]) != 0) {
 648                                                         out << ">" << nameRepresents[i] << endl << currSeq.getAligned() << endl;
 649                                                         count++;
 650                                                 }
 651                                         }
 652                                 }else{
 653                                         m->mothurOut("[ERROR]: " + thisname + " is not in your namefile, please correct."); m->mothurOutEndLine();
 654                                 }
 655                         }
 656                         m->gobble(in);
 657                 }
 658                 in.close();
 659                 out.close();
 660
 661
 662                 if (count != subset.size()) {
 663                         m->mothurOut("[ERROR]: The subset selected contained " + toString(subset.size()) + " sequences, but I only found " + toString(count) + " of those in the fastafile."); m->mothurOutEndLine();
 664                 }
 665
 666                 if (namefile != "") {
 667                         m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
 668                         map<string, string> variables;
 669             variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
 670             variables["[extension]"] = m->getExtension(namefile);
 671             string outputNameFileName = getOutputFileName("name", variables);
 672                         //use unique.seqs to create new name and fastafile
 673                         string inputString = "fasta=" + outputFileName;
 674                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 675                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 676                         m->mothurCalling = true;
 677
 678                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 679                         uniqueCommand->execute();
 680
 681                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 682
 683                         delete uniqueCommand;
 684                         m->mothurCalling = false;
 685
 686             m->renameFile(filenames["name"][0], outputNameFileName);
 687             m->renameFile(filenames["fasta"][0], outputFileName);
 688
 689                         outputTypes["name"].push_back(outputNameFileName);  outputNames.push_back(outputNameFileName);
 690
 691                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 692
 693                         m->mothurOut("Done."); m->mothurOutEndLine();
 694
 695             if (taxonomyfile != "") {
 696                 set<string> tempSubset;
 697                 //get new unique names from fasta file
 698                 //read through fasta file outputting only the names on the subsample list after deconvolute
 699                 ifstream in2;
 700                 m->openInputFile(outputFileName, in2);
 701
 702                 while (!in2.eof()) {
 703                     Sequence seq(in2); m->gobble(in2);
 704                     if (seq.getName() != "") {
 705                         tempSubset.insert(seq.getName());
 706                     }
 707                 }
 708                 in2.close();
 709
 710                 //send that list to getTax
 711                 int tcount = getTax(tempSubset);
 712                 if (tcount != tempSubset.size()) { m->mothurOut("[ERROR]: subsampled fasta file contains " + toString(tempSubset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, please correct."); m->mothurOutEndLine(); }
 713             }
 714                 }else {
 715             if (taxonomyfile != "") {
 716                 int tcount = getTax(subset);
 717                 if (tcount != subset.size()) { m->mothurOut("[ERROR]: subsampled fasta file contains " + toString(subset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, please correct."); m->mothurOutEndLine(); }
 718
 719             }  //should only contain uniques.
 720         }
 721
 722                 outputTypes["fasta"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 723
 724                 //if a groupfile is provided read through the group file only outputting the names on the subsample list
 725                 if (groupfile != "") {
 726
 727                         string groupOutputDir = outputDir;
 728                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
 729             map<string, string> variables;
 730             variables["[filename]"] = groupOutputDir + m->getRootName(m->getSimpleName(groupfile));
 731             variables["[extension]"] = m->getExtension(groupfile);
 732                         string groupOutputFileName = getOutputFileName("group", variables);
 733
 734                         ofstream outGroup;
 735                         m->openOutputFile(groupOutputFileName, outGroup);
 736                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
 737
 738                         ifstream inGroup;
 739                         m->openInputFile(groupfile, inGroup);
 740                         string name, group;
 741
 742                         while(!inGroup.eof()){
 743
 744                                 if (m->control_pressed) { inGroup.close(); outGroup.close(); return 0; }
 745
 746                                 inGroup >> name;        m->gobble(inGroup);                     //read from first column
 747                                 inGroup >> group;                       //read from second column
 748
 749                                 //if this name is in the accnos file
 750                                 if (subset.count(name) != 0) {
 751                                         outGroup << name << '\t' << group << endl;
 752                                         subset.erase(name);
 753                                 }
 754
 755                                 m->gobble(inGroup);
 756                         }
 757                         inGroup.close();
 758                         outGroup.close();
 759
 760                         //sanity check
 761                         if (subset.size() != 0) {
 762                                 m->mothurOut("Your groupfile does not match your fasta file."); m->mothurOutEndLine();
 763                                 for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
 764                                         m->mothurOut("[ERROR]: " + *it + " is missing from your groupfile."); m->mothurOutEndLine();
 765                                 }
 766                         }
 767                 }
 768
 769                 return 0;
 770
 771         }
 772         catch(exception& e) {
 773                 m->errorOut(e, "SubSampleCommand", "getSubSampleFasta");
 774                 exit(1);
 775         }
 776 }
 777 //**********************************************************************************************************************
 778 int SubSampleCommand::getNames() {
 779         try {
 780
 781                 ifstream in;
 782                 m->openInputFile(fastafile, in);
 783
 784                 string thisname;
 785                 while(!in.eof()){
 786
 787                         if (m->control_pressed) { in.close(); return 0; }
 788
 789                         Sequence currSeq(in);
 790                         thisname = currSeq.getName();
 791
 792                         if (thisname != "") {
 793                                 vector<string> temp; temp.push_back(thisname);
 794                                 nameMap[thisname] = temp;
 795                                 names.push_back(thisname);
 796                         }
 797                         m->gobble(in);
 798                 }
 799                 in.close();
 800
 801                 return 0;
 802
 803         }
 804         catch(exception& e) {
 805                 m->errorOut(e, "SubSampleCommand", "getNames");
 806                 exit(1);
 807         }
 808 }
 809 //**********************************************************************************************************************
 810 int SubSampleCommand::readNames() {
 811         try {
 812
 813         nameMap.clear();
 814         m->readNames(namefile, nameMap);
 815
 816         //save names of all sequences
 817         map<string, vector<string> >::iterator it;
 818         for (it = nameMap.begin(); it != nameMap.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { names.push_back((it->second)[i]); } }
 819
 820                 return 0;
 821
 822         }
 823         catch(exception& e) {
 824                 m->errorOut(e, "SubSampleCommand", "readNames");
 825                 exit(1);
 826         }
 827 }
 828 //**********************************************************************************************************************
 829 int SubSampleCommand::getSubSampleShared() {
 830         try {
 831
 832                 InputData* input = new InputData(sharedfile, "sharedfile");
 833                 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
 834                 string lastLabel = lookup[0]->getLabel();
 835
 836                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 837                 set<string> processedLabels;
 838                 set<string> userLabels = labels;
 839
 840                 if (size == 0) { //user has not set size, set size = smallest samples size
 841                         size = lookup[0]->getNumSeqs();
 842                         for (int i = 1; i < lookup.size(); i++) {
 843                                 int thisSize = lookup[i]->getNumSeqs();
 844
 845                                 if (thisSize < size) {  size = thisSize;        }
 846                         }
 847                 }else {
 848                         m->clearGroups();
 849                         Groups.clear();
 850                         vector<SharedRAbundVector*> temp;
 851                         for (int i = 0; i < lookup.size(); i++) {
 852                                 if (lookup[i]->getNumSeqs() < size) {
 853                                         m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
 854                                         delete lookup[i];
 855                                 }else {
 856                                         Groups.push_back(lookup[i]->getGroup());
 857                                         temp.push_back(lookup[i]);
 858                                 }
 859                         }
 860                         lookup = temp;
 861                         m->setGroups(Groups);
 862                 }
 863
 864                 if (lookup.size() == 0) {  m->mothurOut("The size you selected is too large, skipping shared file."); m->mothurOutEndLine(); delete input; return 0; }
 865
 866                 m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
 867
 868                 //as long as you are not at the end of the file or done wih the lines you want
 869                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 870                         if (m->control_pressed) {  delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }  return 0;  }
 871
 872                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 873
 874                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 875
 876                                 processShared(lookup);
 877
 878                                 processedLabels.insert(lookup[0]->getLabel());
 879                                 userLabels.erase(lookup[0]->getLabel());
 880                         }
 881
 882                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 883                                 string saveLabel = lookup[0]->getLabel();
 884
 885                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 886
 887                                 lookup = input->getSharedRAbundVectors(lastLabel);
 888                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 889
 890                                 processShared(lookup);
 891
 892                                 processedLabels.insert(lookup[0]->getLabel());
 893                                 userLabels.erase(lookup[0]->getLabel());
 894
 895                                 //restore real lastlabel to save below
 896                                 lookup[0]->setLabel(saveLabel);
 897                         }
 898
 899                         lastLabel = lookup[0]->getLabel();
 900                         //prevent memory leak
 901                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 902
 903                         //get next line to process
 904                         lookup = input->getSharedRAbundVectors();
 905                 }
 906
 907
 908                 if (m->control_pressed) {   return 0;  }
 909
 910                 //output error messages about any remaining user labels
 911                 set<string>::iterator it;
 912                 bool needToRun = false;
 913                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 914                         m->mothurOut("Your file does not include the label " + *it);
 915                         if (processedLabels.count(lastLabel) != 1) {
 916                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 917                                 needToRun = true;
 918                         }else {
 919                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 920                         }
 921                 }
 922
 923                 //run last label if you need to
 924                 if (needToRun == true)  {
 925                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 926                         lookup = input->getSharedRAbundVectors(lastLabel);
 927
 928                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 929
 930                         processShared(lookup);
 931
 932                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 933                 }
 934
 935                 delete input;
 936
 937                 return 0;
 938
 939         }
 940         catch(exception& e) {
 941                 m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
 942                 exit(1);
 943         }
 944 }
 945 //**********************************************************************************************************************
 946 int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
 947         try {
 948
 949                 //save mothurOut's binLabels to restore for next label
 950                 vector<string> saveBinLabels = m->currentBinLabels;
 951
 952                 string thisOutputDir = outputDir;
 953                 if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
 954         map<string, string> variables;
 955         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
 956         variables["[extension]"] = m->getExtension(sharedfile);
 957         variables["[distance]"] = thislookup[0]->getLabel();
 958                 string outputFileName = getOutputFileName("shared", variables);
 959         SubSample sample;
 960         vector<string> subsampledLabels = sample.getSample(thislookup, size);
 961
 962         if (m->control_pressed) {  return 0; }
 963
 964         ofstream out;
 965                 m->openOutputFile(outputFileName, out);
 966                 outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 967
 968         m->currentBinLabels = subsampledLabels;
 969
 970                 thislookup[0]->printHeaders(out);
 971
 972                 for (int i = 0; i < thislookup.size(); i++) {
 973                         out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
 974                         thislookup[i]->print(out);
 975                 }
 976                 out.close();
 977
 978
 979         //save mothurOut's binLabels to restore for next label
 980                 m->currentBinLabels = saveBinLabels;
 981
 982                 return 0;
 983
 984         }
 985         catch(exception& e) {
 986                 m->errorOut(e, "SubSampleCommand", "processShared");
 987                 exit(1);
 988         }
 989 }
 990 //**********************************************************************************************************************
 991 int SubSampleCommand::getSubSampleList() {
 992         try {
 993
 994                 if (namefile != "") { m->readNames(namefile, nameMap); }
 995
 996                 string thisOutputDir = outputDir;
 997                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 998                 map<string, string> variables;
 999         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
1000         variables["[extension]"] = m->getExtension(listfile);
1001                 string outputFileName = getOutputFileName("list", variables);
1002                 ofstream out;
1003                 m->openOutputFile(outputFileName, out);
1004                 outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1005
1006                 InputData* input = new InputData(listfile, "list");
1007                 ListVector* list = input->getListVector();
1008                 string lastLabel = list->getLabel();
1009
1010         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1011                 set<string> processedLabels;
1012                 set<string> userLabels = labels;
1013
1014                 ofstream outGroup;
1015                 GroupMap groupMap;
1016                 if (groupfile != "") {
1017                         groupMap.readMap(groupfile);
1018
1019                         //takes care of user setting groupNames that are invalid or setting groups=all
1020                         SharedUtil util; vector<string> namesGroups = groupMap.getNamesOfGroups(); util.setGroups(Groups, namesGroups);
1021
1022                         //create outputfiles
1023                         string groupOutputDir = outputDir;
1024                         if (outputDir == "") {  groupOutputDir += m->hasPath(groupfile);  }
1025                         string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
1026                         m->openOutputFile(groupOutputFileName, outGroup);
1027                         outputTypes["group"].push_back(groupOutputFileName);  outputNames.push_back(groupOutputFileName);
1028
1029                         //file mismatch quit
1030                         if (list->getNumSeqs() != groupMap.getNumSeqs()) {
1031                                 m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap.getNumSeqs()) + ", please correct.");
1032                                 m->mothurOutEndLine(); delete list; delete input; out.close(); outGroup.close(); return 0;
1033                         }
1034                 }else if (countfile != "") {
1035             if (ct.hasGroupInfo()) {
1036                 SharedUtil util;
1037                 vector<string> namesGroups = ct.getNamesOfGroups();
1038                 util.setGroups(Groups, namesGroups);
1039             }
1040
1041             //file mismatch quit
1042                         if (list->getNumSeqs() != ct.getNumUniqueSeqs()) {
1043                                 m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your count file contains " + toString(ct.getNumUniqueSeqs()) + " unique sequences, please correct.");
1044                                 m->mothurOutEndLine();
1045                                 return 0;
1046                         }
1047         }
1048
1049                 //make sure that if your picked groups size is not too big
1050                 if (persample) {
1051                         if (size == 0) { //user has not set size, set size = smallest samples size
1052                                 if (countfile == "") { size = groupMap.getNumSeqs(Groups[0]); }
1053                 else {  size = ct.getGroupCount(Groups[0]);  }
1054
1055                                 for (int i = 1; i < Groups.size(); i++) {
1056                                         int thisSize = 0;
1057                     if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
1058                     else {  thisSize = ct.getGroupCount(Groups[i]);  }
1059
1060                                         if (thisSize < size) {  size = thisSize;        }
1061                                 }
1062                         }else { //make sure size is not too large
1063                                 vector<string> newGroups;
1064                                 for (int i = 0; i < Groups.size(); i++) {
1065                                         int thisSize = 0;
1066                     if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
1067                     else {  thisSize = ct.getGroupCount(Groups[i]);  }
1068
1069                                         if (thisSize >= size) { newGroups.push_back(Groups[i]); }
1070                                         else {  m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
1071                                 }
1072                                 Groups = newGroups;
1073                 if (newGroups.size() == 0) {  m->mothurOut("[ERROR]: all groups removed."); m->mothurOutEndLine(); m->control_pressed = true; }
1074                         }
1075
1076                         m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
1077                 }else{
1078             if (pickedGroups) {
1079                                 int total = 0;
1080                                 for(int i = 0; i < Groups.size(); i++) {
1081                     if (countfile == "") { total += groupMap.getNumSeqs(Groups[i]); }
1082                     else {  total += ct.getGroupCount(Groups[i]);  }
1083                                 }
1084
1085                                 if (size == 0) { //user has not set size, set size = 10% samples size
1086                                         size = int (total * 0.10);
1087                                 }
1088
1089                                 if (total < size) {
1090                                         if (size != 0) {
1091                                                 m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
1092                                         }
1093                                         size = int (total * 0.10);
1094                                 }
1095
1096                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
1097                         }else {
1098                 if (size == 0) { //user has not set size, set size = 10% samples size
1099                                         if (countfile == "") {  size = int (list->getNumSeqs() * 0.10);  }
1100                     else { size = int (ct.getNumSeqs() * 0.10);  }
1101                                 }
1102
1103                                 int thisSize = 0;
1104                 if (countfile == "") { thisSize = list->getNumSeqs();  }
1105                 else { thisSize = ct.getNumSeqs(); }
1106
1107                                 if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
1108                                         size = thisSize;
1109                                 }
1110
1111                                 m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine();
1112             }
1113         }
1114
1115         set<string> subset; //dont want repeat sequence names added
1116                 if (countfile == "") {
1117             //fill names
1118             for (int i = 0; i < list->getNumBins(); i++) {
1119                 string binnames = list->get(i);
1120                 vector<string> thisBin;
1121                 m->splitAtComma(binnames, thisBin);
1122
1123                 for(int j=0;j<thisBin.size();j++){
1124                     if (groupfile != "") { //if there is a groupfile given fill in group info
1125                         string group = groupMap.getGroup(thisBin[j]);
1126                         if (group == "not found") { m->mothurOut("[ERROR]: " + thisBin[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
1127
1128                                                 //if hte user picked groups, we only want to keep the names of sequences from those groups
1129                                                 if (pickedGroups) { if (m->inUsersGroups(group, Groups)) { names.push_back(thisBin[j]); }  }
1130                                                 else{ names.push_back(thisBin[j]); }
1131                     }//save everyone, group
1132                     else{ names.push_back(thisBin[j]); }
1133                 }
1134             }
1135
1136             random_shuffle(names.begin(), names.end());
1137
1138             //randomly select a subset of those names to include in the subsample
1139             if (persample) {
1140                 //initialize counts
1141                 map<string, int> groupCounts;
1142                 map<string, int>::iterator itGroupCounts;
1143                 for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
1144
1145                 for (int j = 0; j < names.size(); j++) {
1146
1147                     if (m->control_pressed) { delete list; delete input;  return 0; }
1148
1149                     string group = groupMap.getGroup(names[j]);
1150                     if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
1151                     else{
1152                         itGroupCounts = groupCounts.find(group);
1153                         if (itGroupCounts != groupCounts.end()) {
1154                             if (groupCounts[group] < size) {    subset.insert(names[j]);        groupCounts[group]++; }
1155                         }
1156                     }
1157                 }
1158             }else{
1159                 for (int j = 0; j < size; j++) {
1160                     if (m->control_pressed) { break; }
1161                     subset.insert(names[j]);
1162                 }
1163             }
1164
1165             if (groupfile != "") {
1166                 //write out new groupfile
1167                 for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
1168                     string group = groupMap.getGroup(*it);
1169                     if (group == "not found") { group = "NOTFOUND"; }
1170                     outGroup << *it << '\t' << group << endl;
1171                 }
1172                 outGroup.close();
1173             }
1174                 }else {
1175             SubSample sample; CountTable sampledCt;
1176
1177             if (persample)  { sampledCt = sample.getSample(ct, size, Groups);               }
1178             else            { sampledCt = sample.getSample(ct, size, Groups, pickedGroups); }
1179
1180             vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
1181             for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
1182
1183             string countOutputDir = outputDir;
1184             if (outputDir == "") {  countOutputDir += m->hasPath(countfile);  }
1185             map<string, string> variables;
1186             variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
1187             variables["[extension]"] = m->getExtension(countfile);
1188             string countOutputFileName = getOutputFileName("count", variables);
1189             outputTypes["count"].push_back(countOutputFileName);  outputNames.push_back(countOutputFileName);
1190             sampledCt.printTable(countOutputFileName);
1191         }
1192
1193                 //as long as you are not at the end of the file or done wih the lines you want
1194                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1195
1196                         if (m->control_pressed) {  delete list; delete input;  out.close();  return 0;  }
1197
1198                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
1199
1200                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1201
1202                                 processList(list, out, subset);
1203
1204                                 processedLabels.insert(list->getLabel());
1205                                 userLabels.erase(list->getLabel());
1206                         }
1207
1208                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1209                                 string saveLabel = list->getLabel();
1210
1211                                 delete list;
1212
1213                                 list = input->getListVector(lastLabel);
1214                                 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1215
1216                                 processList(list, out, subset);
1217
1218                                 processedLabels.insert(list->getLabel());
1219                                 userLabels.erase(list->getLabel());
1220
1221                                 //restore real lastlabel to save below
1222                                 list->setLabel(saveLabel);
1223                         }
1224
1225                         lastLabel = list->getLabel();
1226
1227                         delete list; list = NULL;
1228
1229                         //get next line to process
1230                         list = input->getListVector();
1231                 }
1232
1233
1234                 if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); return 0;  }
1235
1236                 //output error messages about any remaining user labels
1237                 set<string>::iterator it;
1238                 bool needToRun = false;
1239                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1240                         m->mothurOut("Your file does not include the label " + *it);
1241                         if (processedLabels.count(lastLabel) != 1) {
1242                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1243                                 needToRun = true;
1244                         }else {
1245                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1246                         }
1247                 }
1248
1249                 //run last label if you need to
1250                 if (needToRun == true)  {
1251                         if (list != NULL) { delete list; }
1252
1253                         list = input->getListVector(lastLabel);
1254
1255                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
1256
1257                         processList(list, out, subset);
1258
1259                         delete list; list = NULL;
1260                 }
1261
1262                 out.close();
1263                 if (list != NULL) { delete list; }
1264                 delete input;
1265
1266         if (taxonomyfile != "") {
1267             if (namefile == "") {
1268                 InputData input(listfile, "list");
1269                 ListVector* list = input.getListVector();
1270                 string lastLabel = list->getLabel();
1271
1272                 for (int i = 0; i < list->getNumBins(); i++) {
1273                     vector<string> temp;
1274                     string bin = list->get(i);
1275                     m->splitAtComma(bin, temp);
1276                     for (int j = 0; j < temp.size(); j++) { vector<string> tempFakeOut; tempFakeOut.push_back(temp[j]); nameMap[temp[j]] = tempFakeOut; }
1277                 }
1278                 delete list;
1279
1280                 int tcount = getTax(subset);
1281                 if (tcount != subset.size()) { m->mothurOut("[ERROR]: subsampled list file contains " + toString(subset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, did you forget a name file? Please correct."); m->mothurOutEndLine(); }
1282             }else {
1283                 string tempAccnos = "temp.accnos";
1284                 ofstream outAccnos;
1285                 m->openOutputFile(tempAccnos, outAccnos);
1286                 for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) { outAccnos << *it << endl; }
1287                 outAccnos.close();
1288
1289                 m->mothurOut("Sampling taxonomy and name file... "); m->mothurOutEndLine();
1290                 string thisNameOutputDir = outputDir;
1291                 if (outputDir == "") {  thisNameOutputDir += m->hasPath(namefile);  }
1292                 map<string, string> variables;
1293                 variables["[filename]"] = thisNameOutputDir + m->getRootName(m->getSimpleName(namefile));
1294                 variables["[extension]"] = m->getExtension(namefile);
1295                 string outputNameFileName = getOutputFileName("name", variables);
1296
1297                 string thisTaxOutputDir = outputDir;
1298                 if (outputDir == "") {  thisTaxOutputDir += m->hasPath(taxonomyfile);  }
1299                 variables["[filename]"] = thisTaxOutputDir + m->getRootName(m->getSimpleName(taxonomyfile));
1300                 variables["[extension]"] = m->getExtension(taxonomyfile);
1301                 string outputTaxFileName = getOutputFileName("taxonomy", variables);
1302
1303
1304                 //use unique.seqs to create new name and fastafile
1305                 string inputString = "dups=f, name=" + namefile + ", taxonomy=" + taxonomyfile + ", accnos=" + tempAccnos;
1306                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
1307                 m->mothurOut("Running command: get.seqs(" + inputString + ")"); m->mothurOutEndLine();
1308                 m->mothurCalling = true;
1309
1310                 Command* getCommand = new GetSeqsCommand(inputString);
1311                 getCommand->execute();
1312
1313                 map<string, vector<string> > filenames = getCommand->getOutputFiles();
1314
1315                 delete getCommand;
1316                 m->mothurCalling = false;
1317
1318                 m->renameFile(filenames["name"][0], outputNameFileName);
1319                 m->renameFile(filenames["taxonomy"][0], outputTaxFileName);
1320
1321                 outputTypes["name"].push_back(outputNameFileName);  outputNames.push_back(outputNameFileName);
1322                 outputNames.push_back(outputTaxFileName); outputTypes["taxonomy"].push_back(outputTaxFileName);
1323
1324                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
1325
1326                 m->mothurOut("Done."); m->mothurOutEndLine();
1327             }
1328         }
1329
1330                 return 0;
1331
1332         }
1333         catch(exception& e) {
1334                 m->errorOut(e, "SubSampleCommand", "getSubSampleList");
1335                 exit(1);
1336         }
1337 }
1338 //**********************************************************************************************************************
1339 int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>& subset) {
1340         try {
1341
1342                 int numBins = list->getNumBins();
1343
1344                 ListVector* temp = new ListVector();
1345                 temp->setLabel(list->getLabel());
1346
1347                 for (int i = 0; i < numBins; i++) {
1348
1349                         if (m->control_pressed) { break; }
1350
1351                         string bin = list->get(i);
1352             vector<string> binnames;
1353             m->splitAtComma(bin, binnames);
1354
1355             string newNames = "";
1356                         for(int j=0;j<binnames.size();j++){ if (subset.count(binnames[j]) != 0) {  newNames += binnames[j] + ",";  } }
1357
1358                         //if there are names in this bin add to new list
1359                         if (newNames != "") {
1360                                 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
1361                                 temp->push_back(newNames);
1362                         }
1363                 }
1364
1365                 delete list;
1366                 list = temp;
1367
1368                 if (m->control_pressed) { return 0; }
1369
1370                 list->print(out);
1371
1372                 return 0;
1373
1374         }
1375         catch(exception& e) {
1376                 m->errorOut(e, "SubSampleCommand", "processList");
1377                 exit(1);
1378         }
1379 }
1380 //**********************************************************************************************************************
1381 int SubSampleCommand::getSubSampleRabund() {
1382         try {
1383                 InputData* input = new InputData(rabundfile, "rabund");
1384                 RAbundVector* rabund = input->getRAbundVector();
1385                 string lastLabel = rabund->getLabel();
1386
1387                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1388                 set<string> processedLabels;
1389                 set<string> userLabels = labels;
1390
1391                 if (size == 0) { //user has not set size, set size = 10%
1392                         size = int((rabund->getNumSeqs()) * 0.10);
1393                 }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; }
1394
1395                 m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1396
1397                 string thisOutputDir = outputDir;
1398                 if (outputDir == "") {  thisOutputDir += m->hasPath(rabundfile);  }
1399         map<string, string> variables;
1400                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile));
1401         variables["[extension]"] = m->getExtension(rabundfile);
1402                 string outputFileName = getOutputFileName("rabund", variables);
1403                 ofstream out;
1404                 m->openOutputFile(outputFileName, out);
1405                 outputTypes["rabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1406
1407                 //as long as you are not at the end of the file or done wih the lines you want
1408                 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1409                         if (m->control_pressed) {  delete input; delete rabund; out.close(); return 0;  }
1410
1411                         if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
1412
1413                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1414
1415                                 processRabund(rabund, out);
1416
1417                                 processedLabels.insert(rabund->getLabel());
1418                                 userLabels.erase(rabund->getLabel());
1419                         }
1420
1421                         if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1422                                 string saveLabel = rabund->getLabel();
1423
1424                                 delete rabund;
1425
1426                                 rabund = input->getRAbundVector(lastLabel);
1427                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1428
1429                                 processRabund(rabund, out);
1430
1431                                 processedLabels.insert(rabund->getLabel());
1432                                 userLabels.erase(rabund->getLabel());
1433
1434                                 //restore real lastlabel to save below
1435                                 rabund->setLabel(saveLabel);
1436                         }
1437
1438                         lastLabel = rabund->getLabel();
1439
1440                         //prevent memory leak
1441                         delete rabund; rabund = NULL;
1442
1443                         //get next line to process
1444                         rabund = input->getRAbundVector();
1445                 }
1446
1447
1448                 if (m->control_pressed) {  out.close(); return 0;  }
1449
1450                 //output error messages about any remaining user labels
1451                 set<string>::iterator it;
1452                 bool needToRun = false;
1453                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1454                         m->mothurOut("Your file does not include the label " + *it);
1455                         if (processedLabels.count(lastLabel) != 1) {
1456                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1457                                 needToRun = true;
1458                         }else {
1459                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1460                         }
1461                 }
1462
1463                 //run last label if you need to
1464                 if (needToRun == true)  {
1465                         if (rabund != NULL) { delete rabund; }
1466
1467                         rabund = input->getRAbundVector(lastLabel);
1468
1469                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
1470
1471                         processRabund(rabund, out);
1472
1473                         delete rabund;
1474                 }
1475
1476                 delete input;
1477                 out.close();
1478
1479                 return 0;
1480
1481         }
1482         catch(exception& e) {
1483                 m->errorOut(e, "SubSampleCommand", "getSubSampleRabund");
1484                 exit(1);
1485         }
1486 }
1487 //**********************************************************************************************************************
1488 int SubSampleCommand::processRabund(RAbundVector*& rabund, ofstream& out) {
1489         try {
1490
1491                 int numBins = rabund->getNumBins();
1492                 int thisSize = rabund->getNumSeqs();
1493
1494                 if (thisSize != size) {
1495
1496                         OrderVector* order = new OrderVector();
1497                         for(int p=0;p<numBins;p++){
1498                                 for(int j=0;j<rabund->get(p);j++){
1499                                         order->push_back(p);
1500                                 }
1501                         }
1502                         random_shuffle(order->begin(), order->end());
1503
1504                         RAbundVector* temp = new RAbundVector(numBins);
1505                         temp->setLabel(rabund->getLabel());
1506
1507                         delete rabund;
1508                         rabund = temp;
1509
1510                         for (int j = 0; j < size; j++) {
1511
1512                                 if (m->control_pressed) { delete order; return 0; }
1513
1514                                 int bin = order->get(j);
1515
1516                                 int abund = rabund->get(bin);
1517                                 rabund->set(bin, (abund+1));
1518                         }
1519
1520                         delete order;
1521                 }
1522
1523                 if (m->control_pressed) { return 0; }
1524
1525                 rabund->print(out);
1526
1527                 return 0;
1528
1529         }
1530         catch(exception& e) {
1531                 m->errorOut(e, "SubSampleCommand", "processRabund");
1532                 exit(1);
1533         }
1534 }
1535 //**********************************************************************************************************************
1536 int SubSampleCommand::getSubSampleSabund() {
1537         try {
1538
1539                 InputData* input = new InputData(sabundfile, "sabund");
1540                 SAbundVector* sabund = input->getSAbundVector();
1541                 string lastLabel = sabund->getLabel();
1542
1543                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
1544                 set<string> processedLabels;
1545                 set<string> userLabels = labels;
1546
1547                 if (size == 0) { //user has not set size, set size = 10%
1548                         size = int((sabund->getNumSeqs()) * 0.10);
1549                 }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; }
1550
1551
1552                 m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine();
1553
1554                 string thisOutputDir = outputDir;
1555                 if (outputDir == "") {  thisOutputDir += m->hasPath(sabundfile);  }
1556         map<string, string> variables;
1557                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile));
1558         variables["[extension]"] = m->getExtension(sabundfile);
1559                 string outputFileName = getOutputFileName("sabund", variables);
1560                 ofstream out;
1561                 m->openOutputFile(outputFileName, out);
1562                 outputTypes["sabund"].push_back(outputFileName);  outputNames.push_back(outputFileName);
1563
1564
1565                 //as long as you are not at the end of the file or done wih the lines you want
1566                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
1567                         if (m->control_pressed) {  delete input; delete sabund; out.close(); return 0;  }
1568
1569                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
1570
1571                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1572
1573                                 processSabund(sabund, out);
1574
1575                                 processedLabels.insert(sabund->getLabel());
1576                                 userLabels.erase(sabund->getLabel());
1577                         }
1578
1579                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
1580                                 string saveLabel = sabund->getLabel();
1581
1582                                 delete sabund;
1583
1584                                 sabund = input->getSAbundVector(lastLabel);
1585                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1586
1587                                 processSabund(sabund, out);
1588
1589                                 processedLabels.insert(sabund->getLabel());
1590                                 userLabels.erase(sabund->getLabel());
1591
1592                                 //restore real lastlabel to save below
1593                                 sabund->setLabel(saveLabel);
1594                         }
1595
1596                         lastLabel = sabund->getLabel();
1597
1598                         //prevent memory leak
1599                         delete sabund; sabund = NULL;
1600
1601                         //get next line to process
1602                         sabund = input->getSAbundVector();
1603                 }
1604
1605
1606                 if (m->control_pressed) {  out.close(); return 0;  }
1607
1608                 //output error messages about any remaining user labels
1609                 set<string>::iterator it;
1610                 bool needToRun = false;
1611                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
1612                         m->mothurOut("Your file does not include the label " + *it);
1613                         if (processedLabels.count(lastLabel) != 1) {
1614                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
1615                                 needToRun = true;
1616                         }else {
1617                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
1618                         }
1619                 }
1620
1621                 //run last label if you need to
1622                 if (needToRun == true)  {
1623                         if (sabund != NULL) { delete sabund; }
1624
1625                         sabund = input->getSAbundVector(lastLabel);
1626
1627                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
1628
1629                         processSabund(sabund, out);
1630
1631                         delete sabund;
1632                 }
1633
1634                 delete input;
1635                 out.close();
1636
1637                 return 0;
1638
1639         }
1640         catch(exception& e) {
1641                 m->errorOut(e, "SubSampleCommand", "getSubSampleSabund");
1642                 exit(1);
1643         }
1644 }
1645 //**********************************************************************************************************************
1646 int SubSampleCommand::processSabund(SAbundVector*& sabund, ofstream& out) {
1647         try {
1648
1649                 RAbundVector* rabund = new RAbundVector();
1650                 *rabund = sabund->getRAbundVector();
1651
1652                 int numBins = rabund->getNumBins();
1653                 int thisSize = rabund->getNumSeqs();
1654
1655                 if (thisSize != size) {
1656
1657                         OrderVector* order = new OrderVector();
1658                         for(int p=0;p<numBins;p++){
1659                                 for(int j=0;j<rabund->get(p);j++){
1660                                         order->push_back(p);
1661                                 }
1662                         }
1663                         random_shuffle(order->begin(), order->end());
1664
1665                         RAbundVector* temp = new RAbundVector(numBins);
1666                         temp->setLabel(rabund->getLabel());
1667
1668                         delete rabund;
1669                         rabund = temp;
1670
1671                         for (int j = 0; j < size; j++) {
1672
1673                                 if (m->control_pressed) { delete order; return 0; }
1674
1675                                 int bin = order->get(j);
1676
1677                                 int abund = rabund->get(bin);
1678                                 rabund->set(bin, (abund+1));
1679                         }
1680
1681                         delete order;
1682                 }
1683
1684                 if (m->control_pressed) { return 0; }
1685
1686                 delete sabund;
1687                 sabund = new SAbundVector();
1688                 *sabund = rabund->getSAbundVector();
1689                 delete rabund;
1690
1691                 sabund->print(out);
1692
1693                 return 0;
1694
1695         }
1696         catch(exception& e) {
1697                 m->errorOut(e, "SubSampleCommand", "processSabund");
1698                 exit(1);
1699         }
1700 }
1701
1702 //**********************************************************************************************************************
1703 int SubSampleCommand::getTax(set<string>& subset) {
1704         try {
1705
1706         string thisTaxOutputDir = outputDir;
1707         if (outputDir == "") {  thisTaxOutputDir += m->hasPath(taxonomyfile);  }
1708         map<string, string> variables;
1709         variables["[filename]"] = thisTaxOutputDir + m->getRootName(m->getSimpleName(taxonomyfile));
1710         variables["[extension]"] = m->getExtension(taxonomyfile);
1711         string outputTaxFileName = getOutputFileName("taxonomy", variables);
1712         ofstream outTax;
1713         m->openOutputFile(outputTaxFileName, outTax);
1714         outputNames.push_back(outputTaxFileName); outputTypes["taxonomy"].push_back(outputTaxFileName);
1715
1716         //read through fasta file outputting only the names on the subsample list
1717         ifstream inTax;
1718         m->openInputFile(taxonomyfile, inTax);
1719
1720         string tname, tax;
1721         int tcount = 0;
1722         map<string, vector<string> >::iterator itNameMap;
1723
1724         while(!inTax.eof()){
1725
1726             if (m->control_pressed) { inTax.close(); outTax.close();  return 0; }
1727
1728             inTax >> tname;     m->gobble(inTax);                       //read from first column
1729             inTax >> tax;       m->gobble(inTax);               //read from second column
1730
1731             //does the subset contain a sequence that this sequence represents
1732             itNameMap = nameMap.find(tname);
1733             if (itNameMap != nameMap.end()) {
1734                 vector<string> nameRepresents = itNameMap->second;
1735
1736
1737                 for (int i = 0; i < nameRepresents.size(); i++){
1738                     if (subset.count(nameRepresents[i]) != 0) {
1739                         outTax << nameRepresents[i] << '\t' << tax << endl;
1740                         tcount++;
1741
1742                     }
1743                 }
1744             }else{ m->mothurOut("[ERROR]: " + tname + " is missing, please correct."); m->mothurOutEndLine(); }
1745         }
1746         inTax.close();
1747         outTax.close();
1748
1749         return tcount;
1750     }
1751     catch(exception& e) {
1752         m->errorOut(e, "SubSampleCommand", "getTax");
1753         exit(1);
1754     }
1755 }
1756
1757 //**********************************************************************************************************************
1758
1759
1760