preclustercommand.cpp

   1 /*
   2  *  preclustercommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 12/21/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "preclustercommand.h"
  11 #include "deconvolutecommand.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> PreClusterCommand::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  19                 CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
  20                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  21                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  22                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  23
  24                 vector<string> myArray;
  25                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  26                 return myArray;
  27         }
  28         catch(exception& e) {
  29                 m->errorOut(e, "PreClusterCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string PreClusterCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The pre.cluster command groups sequences that are within a given number of base mismatches.\n";
  38                 helpString += "The pre.cluster command outputs a new fasta and name file.\n";
  39                 helpString += "The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n";
  40                 helpString += "The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n";
  41                 helpString += "The group parameter allows you to provide a group file so you can cluster by group. \n";
  42                 helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n";
  43                 helpString += "The pre.cluster command should be in the following format: \n";
  44                 helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n";
  45                 helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n";
  46                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  47                 return helpString;
  48         }
  49         catch(exception& e) {
  50                 m->errorOut(e, "PreClusterCommand", "getHelpString");
  51                 exit(1);
  52         }
  53 }
  54
  55 //**********************************************************************************************************************
  56 PreClusterCommand::PreClusterCommand(){
  57         try {
  58                 abort = true; calledHelp = true;
  59                 setParameters();
  60                 vector<string> tempOutNames;
  61                 outputTypes["fasta"] = tempOutNames;
  62                 outputTypes["name"] = tempOutNames;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 PreClusterCommand::PreClusterCommand(string option) {
  72         try {
  73                 abort = false; calledHelp = false;
  74
  75                 //allow user to run help
  76                 if(option == "help") { help(); abort = true; calledHelp = true; }
  77                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  78
  79                 else {
  80                         vector<string> myArray = setParameters();
  81
  82                         OptionParser parser(option);
  83                         map<string, string> parameters = parser.getParameters();
  84
  85                         ValidParameters validParameter;
  86                         map<string, string>::iterator it;
  87
  88                         //check to make sure all parameters are valid for command
  89                         for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
  90                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
  91                         }
  92
  93                         //initialize outputTypes
  94                         vector<string> tempOutNames;
  95                         outputTypes["fasta"] = tempOutNames;
  96                         outputTypes["name"] = tempOutNames;
  97
  98                         //if the user changes the input directory command factory will send this info to us in the output parameter
  99                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 100                         if (inputDir == "not found"){   inputDir = "";          }
 101                         else {
 102                                 string path;
 103                                 it = parameters.find("fasta");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 109                                 }
 110
 111                                 it = parameters.find("name");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 117                                 }
 118
 119                                 it = parameters.find("group");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 125                                 }
 126                         }
 127
 128                         //check for required parameters
 129                         fastafile = validParameter.validFile(parameters, "fasta", true);
 130                         if (fastafile == "not found") {
 131                                 fastafile = m->getFastaFile();
 132                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 133                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 134                         }
 135                         else if (fastafile == "not open") { abort = true; }
 136                         else { m->setFastaFile(fastafile); }
 137
 138                         //if the user changes the output directory command factory will send this info to us in the output parameter
 139                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 140                                 outputDir = "";
 141                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 142                         }
 143
 144                         //check for optional parameter and set defaults
 145                         // ...at some point should added some additional type checking...
 146                         namefile = validParameter.validFile(parameters, "name", true);
 147                         if (namefile == "not found") { namefile =  "";  }
 148                         else if (namefile == "not open") { abort = true; }
 149                         else {  m->setNameFile(namefile); }
 150
 151                         groupfile = validParameter.validFile(parameters, "group", true);
 152                         if (groupfile == "not found") { groupfile =  "";  bygroup = false; }
 153                         else if (groupfile == "not open") { abort = true; groupfile =  ""; }
 154                         else {   m->setGroupFile(groupfile); bygroup = true;  }
 155
 156                         string temp     = validParameter.validFile(parameters, "diffs", false);         if(temp == "not found"){        temp = "1"; }
 157                         convert(temp, diffs);
 158
 159                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 160                         m->setProcessors(temp);
 161                         convert(temp, processors);
 162
 163
 164                 }
 165
 166         }
 167         catch(exception& e) {
 168                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
 169                 exit(1);
 170         }
 171 }
 172 //**********************************************************************************************************************
 173
 174 int PreClusterCommand::execute(){
 175         try {
 176
 177                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 178
 179                 int start = time(NULL);
 180
 181                 string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
 182                 string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile);
 183                 string newNamesFile = fileroot + "precluster.names";
 184
 185                 if (bygroup) {
 186                         //clear out old files
 187                         ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close();
 188                         ofstream outNames; m->openOutputFile(newNamesFile, outNames);  outNames.close();
 189
 190                         //parse fasta and name file by group
 191                         SequenceParser* parser;
 192                         if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile);      }
 193                         else                            { parser = new SequenceParser(groupfile, fastafile);                    }
 194
 195                         vector<string> groups = parser->getNamesOfGroups();
 196
 197 //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 198                         if(processors == 1)     {       driverGroups(parser, newFastaFile, newNamesFile, 0, groups.size(), groups);     }
 199                         else                            {       createProcessesGroups(parser, newFastaFile, newNamesFile, groups);                      }
 200 //#else
 201 //                      driverGroups(parser, newFastaFile, newNamesFile, 0, groups.size(), groups);
 202 //#endif
 203
 204                         delete parser;
 205
 206                         if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
 207
 208                         //run unique.seqs for deconvolute results
 209                         string inputString = "fasta=" + newFastaFile;
 210                         if (namefile != "") { inputString += ", name=" + newNamesFile; }
 211                         m->mothurOutEndLine();
 212                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 213                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 214
 215                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 216                         uniqueCommand->execute();
 217
 218                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 219
 220                         delete uniqueCommand;
 221
 222                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 223
 224                         m->renameFile(filenames["fasta"][0], newFastaFile);
 225
 226                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine();
 227
 228                 }else {
 229                         if (namefile != "") { readNameFile(); }
 230
 231                         //reads fasta file and return number of seqs
 232                         int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
 233
 234                         if (m->control_pressed) { return 0; }
 235
 236                         if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0;  }
 237                         if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0;  }
 238
 239                         int count = process();
 240
 241                         if (m->control_pressed) { return 0; }
 242
 243                         m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 244                         m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 245                         printData(newFastaFile, newNamesFile);
 246
 247                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 248                 }
 249
 250                 if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
 251
 252                 m->mothurOutEndLine();
 253                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 254                 m->mothurOut(newFastaFile); m->mothurOutEndLine();      outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
 255                 m->mothurOut(newNamesFile); m->mothurOutEndLine();      outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);
 256                 m->mothurOutEndLine();
 257
 258                 //set fasta file as new current fastafile
 259                 string current = "";
 260                 itTypes = outputTypes.find("fasta");
 261                 if (itTypes != outputTypes.end()) {
 262                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 263                 }
 264
 265                 itTypes = outputTypes.find("name");
 266                 if (itTypes != outputTypes.end()) {
 267                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 268                 }
 269
 270                 return 0;
 271
 272         }
 273         catch(exception& e) {
 274                 m->errorOut(e, "PreClusterCommand", "execute");
 275                 exit(1);
 276         }
 277 }
 278 /**************************************************************************************************/
 279 int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newFName, string newNName, vector<string> groups) {
 280         try {
 281
 282                 vector<int> processIDS;
 283                 int process = 1;
 284                 int num = 0;
 285
 286                 //sanity check
 287                 if (groups.size() < processors) { processors = groups.size(); }
 288
 289                 //divide the groups between the processors
 290                 vector<linePair> lines;
 291                 int numGroupsPerProcessor = groups.size() / processors;
 292                 for (int i = 0; i < processors; i++) {
 293                         int startIndex =  i * numGroupsPerProcessor;
 294                         int endIndex = (i+1) * numGroupsPerProcessor;
 295                         if(i == (processors - 1)){      endIndex = groups.size();       }
 296                         lines.push_back(linePair(startIndex, endIndex));
 297                 }
 298
 299 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 300
 301                 //loop through and create all the processes you want
 302                 while (process != processors) {
 303                         int pid = fork();
 304
 305                         if (pid > 0) {
 306                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 307                                 process++;
 308                         }else if (pid == 0){
 309                                 num = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
 310                                 exit(0);
 311                         }else {
 312                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 313                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 314                                 exit(0);
 315                         }
 316                 }
 317
 318                 //do my part
 319                 num = driverGroups(parser, newFName, newNName, lines[0].start, lines[0].end, groups);
 320
 321                 //force parent to wait until all the processes are done
 322                 for (int i=0;i<processIDS.size();i++) {
 323                         int temp = processIDS[i];
 324                         wait(&temp);
 325                 }
 326
 327 #else
 328
 329                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 330                 //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
 331                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 332                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 333
 334                 vector<preClusterData*> pDataArray;
 335                 DWORD   dwThreadIdArray[processors-1];
 336                 HANDLE  hThreadArray[processors-1];
 337
 338                 //Create processor worker threads.
 339                 for( int i=1; i<processors; i++ ){
 340                         // Allocate memory for thread data.
 341                         string extension = toString(i) + ".temp";
 342
 343                         preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), groups, m, lines[i].start, lines[i].end, diffs, i);
 344                         pDataArray.push_back(tempPreCluster);
 345                         processIDS.push_back(i);
 346
 347                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 348                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 349                         hThreadArray[i-1] = CreateThread(NULL, 0, MyPreclusterThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 350                 }
 351
 352
 353                 //using the main process as a worker saves time and memory
 354                 num = driverGroups(parser, newFName, newNName, lines[0].start, lines[0].end, groups);
 355
 356                 //Wait until all threads have terminated.
 357                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 358
 359                 //Close all thread handles and free memory allocations.
 360                 for(int i=0; i < pDataArray.size(); i++){
 361                         CloseHandle(hThreadArray[i]);
 362                         delete pDataArray[i];
 363                 }
 364
 365 #endif
 366
 367                 //append output files
 368                 for(int i=0;i<processIDS.size();i++){
 369                         m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
 370                         m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
 371
 372                         m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
 373                         m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
 374                 }
 375
 376                 return num;
 377
 378         }
 379         catch(exception& e) {
 380                 m->errorOut(e, "PreClusterCommand", "createProcessesGroups");
 381                 exit(1);
 382         }
 383 }
 384 /**************************************************************************************************/
 385 int PreClusterCommand::driverGroups(SequenceParser* parser, string newFFile, string newNFile, int start, int end, vector<string> groups){
 386         try {
 387
 388                 int numSeqs = 0;
 389
 390                 //precluster each group
 391                 for (int i = start; i < end; i++) {
 392
 393                         start = time(NULL);
 394
 395                         if (m->control_pressed) {  return 0; }
 396
 397                         m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
 398
 399                         map<string, string> thisNameMap;
 400                         if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); }
 401                         vector<Sequence> thisSeqs = parser->getSeqs(groups[i]);
 402
 403                         //fill alignSeqs with this groups info.
 404                         numSeqs = loadSeqs(thisNameMap, thisSeqs);
 405
 406                         if (m->control_pressed) {   return 0; }
 407
 408                         if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); m->control_pressed = true; return 0;  }
 409
 410                         int count = process();
 411
 412                         if (m->control_pressed) {  return 0; }
 413
 414                         m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 415                         m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 416                         printData(newFFile, newNFile);
 417
 418                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 419
 420                 }
 421
 422                 return numSeqs;
 423         }
 424         catch(exception& e) {
 425                 m->errorOut(e, "PreClusterCommand", "driverGroups");
 426                 exit(1);
 427         }
 428 }
 429 /**************************************************************************************************/
 430 int PreClusterCommand::process(){
 431         try {
 432
 433                 //sort seqs by number of identical seqs
 434                 sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
 435
 436                 int count = 0;
 437                 int numSeqs = alignSeqs.size();
 438
 439                 //think about running through twice...
 440                 for (int i = 0; i < numSeqs; i++) {
 441
 442                         //are you active
 443                         //                      itActive = active.find(alignSeqs[i].seq.getName());
 444
 445                         if (alignSeqs[i].active) {  //this sequence has not been merged yet
 446
 447                                 //try to merge it with all smaller seqs
 448                                 for (int j = i+1; j < numSeqs; j++) {
 449
 450                                         if (m->control_pressed) { return 0; }
 451
 452                                         if (alignSeqs[j].active) {  //this sequence has not been merged yet
 453                                                 //are you within "diff" bases
 454                                                 int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
 455
 456                                                 if (mismatch <= diffs) {
 457                                                         //merge
 458                                                         alignSeqs[i].names += ',' + alignSeqs[j].names;
 459                                                         alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
 460
 461                                                         alignSeqs[j].active = 0;
 462                                                         alignSeqs[j].numIdentical = 0;
 463                                                         count++;
 464                                                 }
 465                                         }//end if j active
 466                                 }//end if i != j
 467
 468                                 //remove from active list
 469                                 alignSeqs[i].active = 0;
 470
 471                         }//end if active i
 472                         if(i % 100 == 0)        { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
 473                 }
 474
 475                 if(numSeqs % 100 != 0)  { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();   }
 476
 477                 return count;
 478
 479         }
 480         catch(exception& e) {
 481                 m->errorOut(e, "PreClusterCommand", "process");
 482                 exit(1);
 483         }
 484 }
 485 /**************************************************************************************************/
 486 int PreClusterCommand::readFASTA(){
 487         try {
 488                 //ifstream inNames;
 489                 ifstream inFasta;
 490
 491                 //m->openInputFile(namefile, inNames);
 492                 m->openInputFile(fastafile, inFasta);
 493
 494                 //string firstCol, secondCol, nameString;
 495                 length = 0;
 496
 497                 while (!inFasta.eof()) {
 498
 499                         if (m->control_pressed) { inFasta.close(); return 0; }
 500
 501                         //inNames >> firstCol >> secondCol;
 502                         //nameString = secondCol;
 503
 504                         //m->gobble(inNames);
 505                         //int size = 1;
 506                         //while (secondCol.find_first_of(',') != -1) {
 507                         //      size++;
 508                         //      secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 509                         //}
 510
 511                         Sequence seq(inFasta);  m->gobble(inFasta);
 512
 513                         if (seq.getName() != "") {  //can get "" if commented line is at end of fasta file
 514                                 if (namefile != "") {
 515                                         itSize = sizes.find(seq.getName());
 516
 517                                         if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
 518                                         else{
 519                                                 seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
 520                                                 alignSeqs.push_back(tempNode);
 521                                                 if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
 522                                         }
 523                                 }else { //no names file, you are identical to yourself
 524                                         seqPNode tempNode(1, seq, seq.getName());
 525                                         alignSeqs.push_back(tempNode);
 526                                         if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
 527                                 }
 528                         }
 529                 }
 530                 inFasta.close();
 531                 //inNames.close();
 532                 return alignSeqs.size();
 533         }
 534
 535         catch(exception& e) {
 536                 m->errorOut(e, "PreClusterCommand", "readFASTA");
 537                 exit(1);
 538         }
 539 }
 540 /**************************************************************************************************/
 541 int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs){
 542         try {
 543                 length = 0;
 544                 alignSeqs.clear();
 545                 map<string, string>::iterator it;
 546                 bool error = false;
 547
 548                 for (int i = 0; i < thisSeqs.size(); i++) {
 549
 550                         if (m->control_pressed) { return 0; }
 551
 552                         if (namefile != "") {
 553                                 it = thisName.find(thisSeqs[i].getName());
 554
 555                                 //should never be true since parser checks for this
 556                                 if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
 557                                 else{
 558                                         //get number of reps
 559                                         int numReps = 1;
 560                                         for(int j=0;j<(it->second).length();j++){
 561                                                 if((it->second)[j] == ','){     numReps++;      }
 562                                         }
 563
 564                                         seqPNode tempNode(numReps, thisSeqs[i], it->second);
 565                                         alignSeqs.push_back(tempNode);
 566                                         if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
 567                                 }
 568                         }else { //no names file, you are identical to yourself
 569                                 seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName());
 570                                 alignSeqs.push_back(tempNode);
 571                                 if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
 572                         }
 573                 }
 574
 575                 //sanity check
 576                 if (error) { m->control_pressed = true; }
 577
 578                 thisSeqs.clear();
 579
 580                 return alignSeqs.size();
 581         }
 582
 583         catch(exception& e) {
 584                 m->errorOut(e, "PreClusterCommand", "loadSeqs");
 585                 exit(1);
 586         }
 587 }
 588
 589 /**************************************************************************************************/
 590
 591 int PreClusterCommand::calcMisMatches(string seq1, string seq2){
 592         try {
 593                 int numBad = 0;
 594
 595                 for (int i = 0; i < seq1.length(); i++) {
 596                         //do they match
 597                         if (seq1[i] != seq2[i]) { numBad++; }
 598                         if (numBad > diffs) { return length;  } //to far to cluster
 599                 }
 600
 601                 return numBad;
 602         }
 603         catch(exception& e) {
 604                 m->errorOut(e, "PreClusterCommand", "calcMisMatches");
 605                 exit(1);
 606         }
 607 }
 608
 609 /**************************************************************************************************/
 610
 611 void PreClusterCommand::printData(string newfasta, string newname){
 612         try {
 613                 ofstream outFasta;
 614                 ofstream outNames;
 615
 616                 if (bygroup) {
 617                         m->openOutputFileAppend(newfasta, outFasta);
 618                         m->openOutputFileAppend(newname, outNames);
 619                 }else {
 620                         m->openOutputFile(newfasta, outFasta);
 621                         m->openOutputFile(newname, outNames);
 622                 }
 623
 624                 for (int i = 0; i < alignSeqs.size(); i++) {
 625                         if (alignSeqs[i].numIdentical != 0) {
 626                                 alignSeqs[i].seq.printSequence(outFasta);
 627                                 outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
 628                         }
 629                 }
 630
 631                 outFasta.close();
 632                 outNames.close();
 633
 634         }
 635         catch(exception& e) {
 636                 m->errorOut(e, "PreClusterCommand", "printData");
 637                 exit(1);
 638         }
 639 }
 640 /**************************************************************************************************/
 641
 642 void PreClusterCommand::readNameFile(){
 643         try {
 644                 ifstream in;
 645                 m->openInputFile(namefile, in);
 646                 string firstCol, secondCol;
 647
 648                 while (!in.eof()) {
 649                         in >> firstCol >> secondCol; m->gobble(in);
 650                         names[firstCol] = secondCol;
 651                         int size = 1;
 652
 653                         for(int i=0;i<secondCol.size();i++){
 654                                 if(secondCol[i] == ','){        size++; }
 655                         }
 656                         sizes[firstCol] = size;
 657                 }
 658                 in.close();
 659         }
 660         catch(exception& e) {
 661                 m->errorOut(e, "PreClusterCommand", "readNameFile");
 662                 exit(1);
 663         }
 664 }
 665
 666 /**************************************************************************************************/
 667
 668