countseqscommand.cpp

   1 /*
   2  *  countseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 6/1/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "countseqscommand.h"
  11 #include "sharedutilities.h"
  12 #include "counttable.h"
  13 #include "inputdata.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> CountSeqsCommand::setParameters(){
  17         try {
  18         CommandParameter pshared("shared", "InputTypes", "", "", "NameSHared-sharedGroup", "NameSHared", "none","count",false,false,true); parameters.push_back(pshared);
  19                 CommandParameter pname("name", "InputTypes", "", "", "NameSHared", "NameSHared", "none","count",false,false,true); parameters.push_back(pname);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
  21         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  22         CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
  23                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  24                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  25                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "CountSeqsCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string CountSeqsCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The count.seqs aka. make.table command reads a name or shared file and outputs a .count_table file.  You may also provide a group with the names file to get the counts broken down by group.\n";
  41                 helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
  42         helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
  43                 helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
  44         helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  45                 helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
  46                 helpString += "Example count.seqs(name=amazon.names) or make.table(name=amazon.names).\n";
  47                 helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourNameFile).\n";
  48                 return helpString;
  49         }
  50         catch(exception& e) {
  51                 m->errorOut(e, "CountSeqsCommand", "getHelpString");
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56 string CountSeqsCommand::getOutputPattern(string type) {
  57     try {
  58         string pattern = "";
  59         if (type == "count") {  pattern = "[filename],count_table-[filename],[distance],count_table"; }
  60         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  61
  62         return pattern;
  63     }
  64     catch(exception& e) {
  65         m->errorOut(e, "CountSeqsCommand", "getOutputPattern");
  66         exit(1);
  67     }
  68 }
  69 //**********************************************************************************************************************
  70 CountSeqsCommand::CountSeqsCommand(){
  71         try {
  72                 abort = true; calledHelp = true;
  73                 setParameters();
  74                 vector<string> tempOutNames;
  75                 outputTypes["count"] = tempOutNames;
  76         }
  77         catch(exception& e) {
  78                 m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
  79                 exit(1);
  80         }
  81 }
  82 //**********************************************************************************************************************
  83
  84 CountSeqsCommand::CountSeqsCommand(string option)  {
  85         try {
  86                 abort = false; calledHelp = false;
  87         allLines = 1;
  88
  89                 //allow user to run help
  90                 if(option == "help") { help(); abort = true; calledHelp = true; }
  91                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  92                 else {
  93                         vector<string> myArray = setParameters();
  94
  95                         OptionParser parser(option);
  96                         map<string,string> parameters = parser.getParameters();
  97
  98                         ValidParameters validParameter;
  99                         map<string,string>::iterator it;
 100
 101                         //check to make sure all parameters are valid for command
 102                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 103                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 104                         }
 105
 106                         //initialize outputTypes
 107                         vector<string> tempOutNames;
 108                         outputTypes["count"] = tempOutNames;
 109
 110
 111                         //if the user changes the input directory command factory will send this info to us in the output parameter
 112                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 113                         if (inputDir == "not found"){   inputDir = "";          }
 114                         else {
 115                                 string path;
 116                                 it = parameters.find("name");
 117                                 //user has given a template file
 118                                 if(it != parameters.end()){
 119                                         path = m->hasPath(it->second);
 120                                         //if the user has not given a path then, add inputdir. else leave path alone.
 121                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 122                                 }
 123
 124                                 it = parameters.find("group");
 125                                 //user has given a template file
 126                                 if(it != parameters.end()){
 127                                         path = m->hasPath(it->second);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 130                                 }
 131
 132                 it = parameters.find("shared");
 133                                 //user has given a template file
 134                                 if(it != parameters.end()){
 135                                         path = m->hasPath(it->second);
 136                                         //if the user has not given a path then, add inputdir. else leave path alone.
 137                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 138                                 }
 139                         }
 140
 141                         //check for required parameters
 142                         namefile = validParameter.validFile(parameters, "name", true);
 143                         if (namefile == "not open") { namefile = ""; abort = true; }
 144                         else if (namefile == "not found"){      namefile = ""; }
 145             else { m->setNameFile(namefile); }
 146
 147             sharedfile = validParameter.validFile(parameters, "shared", true);
 148                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 149                         else if (sharedfile == "not found"){    sharedfile = ""; }
 150             else { m->setSharedFile(sharedfile); }
 151
 152                         groupfile = validParameter.validFile(parameters, "group", true);
 153                         if (groupfile == "not open") { abort = true; }
 154                         else if (groupfile == "not found") {  groupfile = "";  }
 155                         else { m->setGroupFile(groupfile); }
 156
 157             if ((namefile == "") && (sharedfile == "")) {
 158                 namefile = m->getNameFile();
 159                                 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 160                                 else {
 161                     sharedfile = m->getSharedFile();
 162                     if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 163                     else {
 164                         m->mothurOut("You have no current namefile or sharedfile and the name or shared parameter is required."); m->mothurOutEndLine(); abort = true;
 165                     }
 166                 }
 167                         }
 168
 169                         groups = validParameter.validFile(parameters, "groups", false);
 170                         if (groups == "not found") { groups = "all"; }
 171                         m->splitAtDash(groups, Groups);
 172             m->setGroups(Groups);
 173
 174             string temp = validParameter.validFile(parameters, "large", false);         if (temp == "not found") {      temp = "F";     }
 175                         large = m->isTrue(temp);
 176
 177             temp = validParameter.validFile(parameters, "processors", false);   if (temp == "not found"){       temp = m->getProcessors();      }
 178                         m->setProcessors(temp);
 179                         m->mothurConvert(temp, processors);
 180
 181                         //if the user changes the output directory command factory will send this info to us in the output parameter
 182                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 183
 184                 }
 185
 186         }
 187         catch(exception& e) {
 188                 m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
 189                 exit(1);
 190         }
 191 }
 192 //**********************************************************************************************************************
 193
 194 int CountSeqsCommand::execute(){
 195         try {
 196
 197                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 198
 199         map<string, string> variables;
 200
 201         if (namefile != "") {
 202             int total = 0;
 203             int start = time(NULL);
 204             if (outputDir == "") { outputDir = m->hasPath(namefile); }
 205             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
 206             string outputFileName = getOutputFileName("count", variables);
 207
 208             if (!large) { total = processSmall(outputFileName); }
 209             else { total = processLarge(outputFileName);  }
 210
 211             if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
 212
 213             m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create a table for " + toString(total) + " sequences.");
 214             m->mothurOutEndLine(); m->mothurOutEndLine();
 215
 216             m->mothurOutEndLine();
 217             m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
 218
 219         }else {
 220             if (outputDir == "") { outputDir = m->hasPath(sharedfile); }
 221             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
 222
 223             InputData input(sharedfile, "sharedfile");
 224             vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 225             string lastLabel = lookup[0]->getLabel();
 226
 227             //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 228             set<string> processedLabels;
 229             set<string> userLabels = labels;
 230
 231             //as long as you are not at the end of the file or done wih the lines you want
 232             while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 233
 234                 if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
 235
 236                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 237
 238                     m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 239
 240                     processShared(lookup, variables);
 241
 242                     processedLabels.insert(lookup[0]->getLabel());
 243                     userLabels.erase(lookup[0]->getLabel());
 244                 }
 245
 246                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 247                     string saveLabel = lookup[0]->getLabel();
 248
 249                     for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 250                     lookup = input.getSharedRAbundVectors(lastLabel);
 251                     m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 252
 253                     processShared(lookup, variables);
 254
 255                     processedLabels.insert(lookup[0]->getLabel());
 256                     userLabels.erase(lookup[0]->getLabel());
 257
 258                     //restore real lastlabel to save below
 259                     lookup[0]->setLabel(saveLabel);
 260                 }
 261
 262                 lastLabel = lookup[0]->getLabel();
 263                 //prevent memory leak
 264                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 265
 266                 if (m->control_pressed) { return 0; }
 267
 268                 //get next line to process
 269                 lookup = input.getSharedRAbundVectors();
 270             }
 271
 272             if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); }  return 0; }
 273
 274             //output error messages about any remaining user labels
 275             set<string>::iterator it;
 276             bool needToRun = false;
 277             for (it = userLabels.begin(); it != userLabels.end(); it++) {
 278                 m->mothurOut("Your file does not include the label " + *it);
 279                 if (processedLabels.count(lastLabel) != 1) {
 280                     m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 281                     needToRun = true;
 282                 }else {
 283                     m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 284                 }
 285             }
 286
 287             //run last label if you need to
 288             if (needToRun == true)  {
 289                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 290                 lookup = input.getSharedRAbundVectors(lastLabel);
 291
 292                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 293
 294                 processShared(lookup, variables);
 295
 296                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 297             }
 298
 299         }
 300
 301         //set rabund file as new current rabundfile
 302                 itTypes = outputTypes.find("count");
 303                 if (itTypes != outputTypes.end()) {
 304                         if ((itTypes->second).size() != 0) { string current = (itTypes->second)[0]; m->setCountTableFile(current); }
 305                 }
 306
 307         m->mothurOutEndLine();
 308                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 309                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 310                 m->mothurOutEndLine();
 311
 312                 return 0;
 313         }
 314
 315         catch(exception& e) {
 316                 m->errorOut(e, "CountSeqsCommand", "execute");
 317                 exit(1);
 318         }
 319 }
 320 //**********************************************************************************************************************
 321
 322 int CountSeqsCommand::processShared(vector<SharedRAbundVector*>& lookup, map<string, string> variables){
 323     try {
 324         variables["[distance]"] = lookup[0]->getLabel();
 325         string outputFileName = getOutputFileName("count", variables);
 326         outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
 327
 328         ofstream out;
 329         m->openOutputFile(outputFileName, out);
 330
 331         out << "OTU_Label\ttotal\t";
 332         for (int i = 0; i < lookup.size(); i++) { out << lookup[i]->getGroup() << '\t'; } out << endl;
 333
 334         for (int j = 0; j < lookup[0]->getNumBins(); j++) {
 335             if (m->control_pressed) { break; }
 336
 337             int total = 0;
 338             string output = "";
 339             for (int i = 0; i < lookup.size(); i++) {
 340                 total += lookup[i]->getAbundance(j);
 341                 output += toString(lookup[i]->getAbundance(j)) + '\t';
 342             }
 343             out << m->currentSharedBinLabels[j] << '\t' << total << '\t' << output << endl;
 344         }
 345         out.close();
 346
 347         return 0;
 348     }
 349     catch(exception& e) {
 350         m->errorOut(e, "CountSeqsCommand", "processShared");
 351         exit(1);
 352     }
 353 }
 354 //**********************************************************************************************************************
 355
 356 int CountSeqsCommand::processSmall(string outputFileName){
 357         try {
 358         ofstream out;
 359         m->openOutputFile(outputFileName, out); outputTypes["count"].push_back(outputFileName);
 360         outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
 361                 out << "Representative_Sequence\ttotal\t";
 362
 363         GroupMap* groupMap;
 364                 if (groupfile != "") {
 365                         groupMap = new GroupMap(groupfile); groupMap->readMap();
 366
 367                         //make sure groups are valid. takes care of user setting groupNames that are invalid or setting groups=all
 368                         SharedUtil* util = new SharedUtil();
 369                         vector<string> nameGroups = groupMap->getNamesOfGroups();
 370                         util->setGroups(Groups, nameGroups);
 371                         delete util;
 372
 373                         //sort groupNames so that the group title match the counts below, this is needed because the map object automatically sorts
 374                         sort(Groups.begin(), Groups.end());
 375
 376                         //print groupNames
 377                         for (int i = 0; i < Groups.size(); i++) {
 378                                 out << Groups[i] << '\t';
 379                         }
 380                 }
 381                 out << endl;
 382         out.close();
 383
 384         int total = createProcesses(groupMap, outputFileName);
 385
 386         if (groupfile != "") { delete groupMap; }
 387
 388         return total;
 389     }
 390         catch(exception& e) {
 391                 m->errorOut(e, "CountSeqsCommand", "processSmall");
 392                 exit(1);
 393         }
 394 }
 395 /**************************************************************************************************/
 396 int CountSeqsCommand::createProcesses(GroupMap*& groupMap, string outputFileName) {
 397         try {
 398
 399                 vector<int> processIDS;
 400                 int process = 0;
 401         vector<unsigned long long> positions;
 402         vector<linePair> lines;
 403         int numSeqs = 0;
 404
 405 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 406                 positions = m->divideFilePerLine(namefile, processors);
 407                 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
 408 #else
 409                 if(processors == 1){ lines.push_back(linePair(0, 1000));  }
 410         else {
 411             int numSeqs = 0;
 412             positions = m->setFilePosEachLine(namefile, numSeqs);
 413             if (positions.size() < processors) { processors = positions.size(); }
 414
 415             //figure out how many sequences you have to process
 416             int numSeqsPerProcessor = numSeqs / processors;
 417             for (int i = 0; i < processors; i++) {
 418                 int startIndex =  i * numSeqsPerProcessor;
 419                 if(i == (processors - 1)){      numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 420                 lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 421             }
 422         }
 423 #endif
 424
 425
 426 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 427
 428                 //loop through and create all the processes you want
 429                 while (process != processors-1) {
 430                         int pid = fork();
 431
 432                         if (pid > 0) {
 433                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 434                                 process++;
 435                         }else if (pid == 0){
 436                 string filename = toString(getpid()) + ".temp";
 437                                 numSeqs = driver(lines[process].start, lines[process].end, filename, groupMap);
 438
 439                 string tempFile = toString(getpid()) + ".num.temp";
 440                 ofstream outTemp;
 441                 m->openOutputFile(tempFile, outTemp);
 442
 443                 outTemp << numSeqs << endl;
 444                 outTemp.close();
 445
 446                                 exit(0);
 447                         }else {
 448                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 449                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 450                                 exit(0);
 451                         }
 452                 }
 453
 454                 string filename = toString(getpid()) + ".temp";
 455         numSeqs = driver(lines[processors-1].start, lines[processors-1].end, filename, groupMap);
 456
 457                 //force parent to wait until all the processes are done
 458                 for (int i=0;i<processIDS.size();i++) {
 459                         int temp = processIDS[i];
 460                         wait(&temp);
 461                 }
 462
 463         for (int i = 0; i < processIDS.size(); i++) {
 464             string tempFile = toString(processIDS[i]) +  ".num.temp";
 465             ifstream intemp;
 466             m->openInputFile(tempFile, intemp);
 467
 468             int num;
 469             intemp >> num; intemp.close();
 470             numSeqs += num;
 471             m->mothurRemove(tempFile);
 472         }
 473 #else
 474                 vector<countData*> pDataArray;
 475                 DWORD   dwThreadIdArray[processors-1];
 476                 HANDLE  hThreadArray[processors-1];
 477         vector<GroupMap*> copies;
 478
 479                 //Create processor worker threads.
 480                 for( int i=0; i<processors-1; i++ ){
 481                         string filename = toString(i) + ".temp";
 482
 483             GroupMap* copyGroup = new GroupMap();
 484             copyGroup->getCopy(groupMap);
 485             copies.push_back(copyGroup);
 486             vector<string> cGroups = Groups;
 487
 488                         countData* temp = new countData(filename, copyGroup, m, lines[i].start, lines[i].end, groupfile, namefile, cGroups);
 489                         pDataArray.push_back(temp);
 490                         processIDS.push_back(i);
 491
 492                         hThreadArray[i] = CreateThread(NULL, 0, MyCountThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 493                 }
 494
 495                 string filename = toString(processors-1) + ".temp";
 496         numSeqs = driver(lines[processors-1].start, lines[processors-1].end, filename, groupMap);
 497
 498                 //Wait until all threads have terminated.
 499                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 500
 501                 //Close all thread handles and free memory allocations.
 502                 for(int i=0; i < pDataArray.size(); i++){
 503             numSeqs += pDataArray[i]->total;
 504             delete copies[i];
 505                         CloseHandle(hThreadArray[i]);
 506                         delete pDataArray[i];
 507                 }
 508 #endif
 509
 510                 //append output files
 511                 for(int i=0;i<processIDS.size();i++){
 512                         m->appendFiles((toString(processIDS[i]) + ".temp"), outputFileName);
 513                         m->mothurRemove((toString(processIDS[i]) + ".temp"));
 514                 }
 515         m->appendFiles(filename, outputFileName);
 516         m->mothurRemove(filename);
 517
 518
 519         //sanity check
 520         if (groupfile != "") {
 521             if (numSeqs != groupMap->getNumSeqs()) {
 522                 m->mothurOut("[ERROR]: processes reported processing " + toString(numSeqs) + " sequences, but group file indicates you have " + toString(groupMap->getNumSeqs()) + " sequences.");
 523                 if (processors == 1) { m->mothurOut(" Could you have a file mismatch?\n"); }
 524                 else { m->mothurOut(" Either you have a file mismatch or a process failed to complete the task assigned to it.\n"); m->control_pressed = true; }
 525             }
 526                 }
 527                 return numSeqs;
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "CountSeqsCommand", "createProcesses");
 531                 exit(1);
 532         }
 533 }
 534 /**************************************************************************************************/
 535 int CountSeqsCommand::driver(unsigned long long start, unsigned long long end, string outputFileName, GroupMap*& groupMap) {
 536         try {
 537
 538         ofstream out;
 539         m->openOutputFile(outputFileName, out);
 540
 541         ifstream in;
 542                 m->openInputFile(namefile, in);
 543                 in.seekg(start);
 544
 545                 bool done = false;
 546         int total = 0;
 547                 while (!done) {
 548                         if (m->control_pressed) { break; }
 549
 550                         string firstCol, secondCol;
 551                         in >> firstCol; m->gobble(in); in >> secondCol; m->gobble(in);
 552             //cout << firstCol << '\t' << secondCol << endl;
 553             m->checkName(firstCol);
 554             m->checkName(secondCol);
 555                         //cout << firstCol << '\t' << secondCol << endl;
 556
 557                         vector<string> names;
 558                         m->splitAtChar(secondCol, names, ',');
 559
 560                         if (groupfile != "") {
 561                                 //set to 0
 562                                 map<string, int> groupCounts;
 563                                 int total = 0;
 564                                 for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
 565
 566                                 //get counts for each of the users groups
 567                                 for (int i = 0; i < names.size(); i++) {
 568                                         string group = groupMap->getGroup(names[i]);
 569
 570                                         if (group == "not found") { m->mothurOut("[ERROR]: " + names[i] + " is not in your groupfile, please correct."); m->mothurOutEndLine(); }
 571                                         else {
 572                                                 map<string, int>::iterator it = groupCounts.find(group);
 573
 574                                                 //if not found, then this sequence is not from a group we care about
 575                                                 if (it != groupCounts.end()) {
 576                                                         it->second++;
 577                                                         total++;
 578                                                 }
 579                                         }
 580                                 }
 581
 582                                 if (total != 0) {
 583                                         out << firstCol << '\t' << total << '\t';
 584                                         for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 585                                                 out << it->second << '\t';
 586                                         }
 587                                         out << endl;
 588                                 }
 589                         }else {
 590                                 out << firstCol << '\t' << names.size() << endl;
 591                         }
 592
 593                         total += names.size();
 594
 595 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 596             unsigned long long pos = in.tellg();
 597             if ((pos == -1) || (pos >= end)) { break; }
 598 #else
 599             if (in.eof()) { break; }
 600 #endif
 601
 602                 }
 603                 in.close();
 604         out.close();
 605
 606         return total;
 607
 608     }
 609         catch(exception& e) {
 610                 m->errorOut(e, "CountSeqsCommand", "driver");
 611                 exit(1);
 612         }
 613 }
 614 //**********************************************************************************************************************
 615
 616 int CountSeqsCommand::processLarge(string outputFileName){
 617         try {
 618         set<string> namesOfGroups;
 619         map<string, int> initial;
 620         for (set<string>::iterator it = namesOfGroups.begin(); it != namesOfGroups.end(); it++) { initial[(*it)] = 0;  }
 621         ofstream out;
 622         m->openOutputFile(outputFileName, out);
 623         outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
 624                 out << "Representative_Sequence\ttotal\t";
 625         if (groupfile == "") { out << endl; }
 626
 627         map<string, unsigned long long> namesToIndex;
 628         string outfile = m->getRootName(groupfile) + "sorted.groups.temp";
 629         string outName = m->getRootName(namefile) + "sorted.name.temp";
 630         map<int, string> indexToName;
 631         map<int, string> indexToGroup;
 632         if (groupfile != "") {
 633             time_t estart = time(NULL);
 634             //convert name file to redundant -> unique.  set unique name equal to index so we can use vectors, save name for later.
 635             string newNameFile = m->getRootName(namefile) + ".name.temp";
 636             string newGroupFile = m->getRootName(groupfile) + ".group.temp";
 637             indexToName = processNameFile(newNameFile);
 638             indexToGroup = getGroupNames(newGroupFile, namesOfGroups);
 639
 640             //sort file by first column so the names of sequences will be easier to find
 641             //use the unix sort
 642             #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 643                 string command = "sort -n " + newGroupFile + " -o " + outfile;
 644                 system(command.c_str());
 645                 command = "sort -n " + newNameFile + " -o " + outName;
 646                 system(command.c_str());
 647             #else //sort using windows sort
 648                 string command = "sort " + newGroupFile + " /O " + outfile;
 649                 system(command.c_str());
 650                 command = "sort " + newNameFile + " /O " + outName;
 651                 system(command.c_str());
 652             #endif
 653             m->mothurRemove(newNameFile);
 654             m->mothurRemove(newGroupFile);
 655
 656             m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort and index the group and name files. "); m->mothurOutEndLine();
 657         }else { outName = namefile; }
 658
 659         time_t estart = time(NULL);
 660         //open input file
 661                 ifstream in;
 662                 m->openInputFile(outName, in);
 663
 664         //open input file
 665                 ifstream in2;
 666
 667                 int total = 0;
 668         vector< vector<int> > nameMapCount;
 669         if (groupfile != "") {
 670             m->openInputFile(outfile, in2);
 671             nameMapCount.resize(indexToName.size());
 672             for (int i = 0; i < nameMapCount.size(); i++) {
 673                 nameMapCount[i].resize(indexToGroup.size(), 0);
 674             }
 675         }
 676
 677                 while (!in.eof()) {
 678                         if (m->control_pressed) { break; }
 679
 680                         string firstCol;
 681                         in >> firstCol;  m->gobble(in);
 682
 683                         if (groupfile != "") {
 684                 int uniqueIndex;
 685                 in >> uniqueIndex; m->gobble(in);
 686
 687                 string name; int groupIndex;
 688                 in2 >> name >> groupIndex; m->gobble(in2);
 689
 690                 if (name != firstCol) { m->mothurOut("[ERROR]: found " + name + " in your groupfile, but " + firstCol + " was in your namefile, please correct.\n"); m->control_pressed = true; }
 691
 692                 nameMapCount[uniqueIndex][groupIndex]++;
 693                 total++;
 694             }else {
 695                 string secondCol;
 696                 in >> secondCol; m->gobble(in);
 697                 int num = m->getNumNames(secondCol);
 698                 out << firstCol << '\t' << num << endl;
 699                 total += num;
 700             }
 701                 }
 702                 in.close();
 703
 704         if (groupfile != "") {
 705             m->mothurRemove(outfile);
 706             m->mothurRemove(outName);
 707             in2.close();
 708             for (map<int, string>::iterator it = indexToGroup.begin(); it != indexToGroup.end(); it++) { out << it->second << '\t';  }
 709             out << endl;
 710             for (int i = 0; i < nameMapCount.size(); i++) {
 711                 string totalsLine = "";
 712                 int seqTotal = 0;
 713                 for (int j = 0; j < nameMapCount[i].size(); j++) {
 714                     seqTotal += nameMapCount[i][j];
 715                     totalsLine += toString(nameMapCount[i][j]) + '\t';
 716                 }
 717                 out << indexToName[i] << '\t' << seqTotal << '\t' << totalsLine << endl;
 718             }
 719         }
 720
 721         out.close();
 722
 723         m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to create the count table file. "); m->mothurOutEndLine();
 724
 725         return total;
 726     }
 727         catch(exception& e) {
 728                 m->errorOut(e, "CountSeqsCommand", "processLarge");
 729                 exit(1);
 730         }
 731 }
 732 /**************************************************************************************************/
 733 map<int, string> CountSeqsCommand::processNameFile(string name) {
 734         try {
 735         map<int, string> indexToNames;
 736
 737         ofstream out;
 738         m->openOutputFile(name, out);
 739
 740         //open input file
 741                 ifstream in;
 742                 m->openInputFile(namefile, in);
 743
 744         string rest = "";
 745         char buffer[4096];
 746         bool pairDone = false;
 747         bool columnOne = true;
 748         string firstCol, secondCol;
 749         int count = 0;
 750
 751                 while (!in.eof()) {
 752                         if (m->control_pressed) { break; }
 753
 754             in.read(buffer, 4096);
 755             vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
 756
 757             for (int i = 0; i < pieces.size(); i++) {
 758                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
 759                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
 760
 761                 if (pairDone) {
 762                     m->checkName(firstCol);
 763                     m->checkName(secondCol);
 764                     //parse names into vector
 765                     vector<string> theseNames;
 766                     m->splitAtComma(secondCol, theseNames);
 767                     for (int i = 0; i < theseNames.size(); i++) {  out << theseNames[i] << '\t' << count << endl;  }
 768                     indexToNames[count] = firstCol;
 769                     pairDone = false;
 770                     count++;
 771                 }
 772             }
 773                 }
 774                 in.close();
 775
 776
 777         if (rest != "") {
 778             vector<string> pieces = m->splitWhiteSpace(rest);
 779
 780             for (int i = 0; i < pieces.size(); i++) {
 781                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
 782                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
 783
 784                 if (pairDone) {
 785                     m->checkName(firstCol);
 786                     m->checkName(secondCol);
 787                     //parse names into vector
 788                     vector<string> theseNames;
 789                     m->splitAtComma(secondCol, theseNames);
 790                     for (int i = 0; i < theseNames.size(); i++) {  out << theseNames[i] << '\t' << count << endl;  }
 791                     indexToNames[count] = firstCol;
 792                     pairDone = false;
 793                     count++;
 794                 }
 795             }
 796
 797         }
 798         out.close();
 799
 800         return indexToNames;
 801     }
 802         catch(exception& e) {
 803                 m->errorOut(e, "CountSeqsCommand", "processNameFile");
 804                 exit(1);
 805         }
 806 }
 807 /**************************************************************************************************/
 808 map<int, string> CountSeqsCommand::getGroupNames(string filename, set<string>& namesOfGroups) {
 809         try {
 810         map<int, string> indexToGroups;
 811         map<string, int> groupIndex;
 812         map<string, int>::iterator it;
 813
 814         ofstream out;
 815         m->openOutputFile(filename, out);
 816
 817         //open input file
 818                 ifstream in;
 819                 m->openInputFile(groupfile, in);
 820
 821         string rest = "";
 822         char buffer[4096];
 823         bool pairDone = false;
 824         bool columnOne = true;
 825         string firstCol, secondCol;
 826         int count = 0;
 827
 828                 while (!in.eof()) {
 829                         if (m->control_pressed) { break; }
 830
 831             in.read(buffer, 4096);
 832             vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
 833
 834             for (int i = 0; i < pieces.size(); i++) {
 835                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
 836                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
 837
 838                 if (pairDone) {
 839                     m->checkName(firstCol);
 840                     it = groupIndex.find(secondCol);
 841                     if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
 842                         groupIndex[secondCol] = count;
 843                         count++;
 844                     }
 845                     out << firstCol << '\t' << groupIndex[secondCol] << endl;
 846                     namesOfGroups.insert(secondCol);
 847                     pairDone = false;
 848                 }
 849             }
 850                 }
 851                 in.close();
 852
 853
 854         if (rest != "") {
 855             vector<string> pieces = m->splitWhiteSpace(rest);
 856
 857             for (int i = 0; i < pieces.size(); i++) {
 858                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
 859                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
 860
 861                 if (pairDone) {
 862                     m->checkName(firstCol);
 863                     it = groupIndex.find(secondCol);
 864                     if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
 865                         groupIndex[secondCol] = count;
 866                         count++;
 867                     }
 868                     out << firstCol << '\t' << groupIndex[secondCol] << endl;
 869                     namesOfGroups.insert(secondCol);
 870                     pairDone = false;
 871                 }
 872             }
 873         }
 874         out.close();
 875
 876         for (it = groupIndex.begin(); it != groupIndex.end(); it++) {  indexToGroups[it->second] = it->first;  }
 877
 878         return indexToGroups;
 879         }
 880         catch(exception& e) {
 881                 m->errorOut(e, "CountSeqsCommand", "getGroupNames");
 882                 exit(1);
 883         }
 884 }
 885 //**********************************************************************************************************************
 886
 887
 888