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