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 string PreClusterCommand::getOutputFileNameTag(string type, string inputName=""){
  56         try {
  57         string outputFileName = "";
  58                 map<string, vector<string> >::iterator it;
  59
  60         //is this a type this command creates
  61         it = outputTypes.find(type);
  62         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  63         else {
  64             if (type == "fasta") {  outputFileName =  "precluster" + m->getExtension(inputName); }
  65             else if (type == "name") {  outputFileName =  "precluster.names"; }
  66             else if (type == "map") {  outputFileName =  "precluster.map"; }
  67             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  68         }
  69         return outputFileName;
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "PreClusterCommand", "getOutputFileNameTag");
  73                 exit(1);
  74         }
  75 }
  76 //**********************************************************************************************************************
  77 PreClusterCommand::PreClusterCommand(){
  78         try {
  79                 abort = true; calledHelp = true;
  80                 setParameters();
  81                 vector<string> tempOutNames;
  82                 outputTypes["fasta"] = tempOutNames;
  83                 outputTypes["name"] = tempOutNames;
  84                 outputTypes["map"] = tempOutNames;
  85         }
  86         catch(exception& e) {
  87                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
  88                 exit(1);
  89         }
  90 }
  91 //**********************************************************************************************************************
  92
  93 PreClusterCommand::PreClusterCommand(string option) {
  94         try {
  95                 abort = false; calledHelp = false;
  96
  97                 //allow user to run help
  98                 if(option == "help") { help(); abort = true; calledHelp = true; }
  99                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 100
 101                 else {
 102                         vector<string> myArray = setParameters();
 103
 104                         OptionParser parser(option);
 105                         map<string, string> parameters = parser.getParameters();
 106
 107                         ValidParameters validParameter;
 108                         map<string, string>::iterator it;
 109
 110                         //check to make sure all parameters are valid for command
 111                         for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
 112                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 113                         }
 114
 115                         //initialize outputTypes
 116                         vector<string> tempOutNames;
 117                         outputTypes["fasta"] = tempOutNames;
 118                         outputTypes["name"] = tempOutNames;
 119                         outputTypes["map"] = tempOutNames;
 120
 121                         //if the user changes the input directory command factory will send this info to us in the output parameter
 122                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 123                         if (inputDir == "not found"){   inputDir = "";          }
 124                         else {
 125                                 string path;
 126                                 it = parameters.find("fasta");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 132                                 }
 133
 134                                 it = parameters.find("name");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 140                                 }
 141
 142                                 it = parameters.find("group");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 148                                 }
 149                         }
 150
 151                         //check for required parameters
 152                         fastafile = validParameter.validFile(parameters, "fasta", true);
 153                         if (fastafile == "not found") {
 154                                 fastafile = m->getFastaFile();
 155                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 156                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 157                         }
 158                         else if (fastafile == "not open") { abort = true; }
 159                         else { m->setFastaFile(fastafile); }
 160
 161                         //if the user changes the output directory command factory will send this info to us in the output parameter
 162                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 163                                 outputDir = "";
 164                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 165                         }
 166
 167                         //check for optional parameter and set defaults
 168                         // ...at some point should added some additional type checking...
 169                         namefile = validParameter.validFile(parameters, "name", true);
 170                         if (namefile == "not found") { namefile =  "";  }
 171                         else if (namefile == "not open") { namefile = ""; abort = true; }
 172                         else {  m->setNameFile(namefile); }
 173
 174                         groupfile = validParameter.validFile(parameters, "group", true);
 175                         if (groupfile == "not found") { groupfile =  "";  bygroup = false; }
 176                         else if (groupfile == "not open") { abort = true; groupfile =  ""; }
 177                         else {   m->setGroupFile(groupfile); bygroup = true;  }
 178
 179                         string temp     = validParameter.validFile(parameters, "diffs", false);         if(temp == "not found"){        temp = "1"; }
 180                         m->mothurConvert(temp, diffs);
 181
 182                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 183                         m->setProcessors(temp);
 184                         m->mothurConvert(temp, processors);
 185
 186                         if (namefile == "") {
 187                                 vector<string> files; files.push_back(fastafile);
 188                                 parser.getNameFile(files);
 189                         }
 190                 }
 191
 192         }
 193         catch(exception& e) {
 194                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
 195                 exit(1);
 196         }
 197 }
 198 //**********************************************************************************************************************
 199
 200 int PreClusterCommand::execute(){
 201         try {
 202
 203                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 204
 205                 int start = time(NULL);
 206
 207                 string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
 208                 string newFastaFile = fileroot + getOutputFileNameTag("fasta", fastafile);
 209                 string newNamesFile = fileroot + getOutputFileNameTag("name");
 210                 string newMapFile = fileroot + getOutputFileNameTag("map"); //add group name if by group
 211                 outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
 212                 outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);
 213
 214
 215                 if (bygroup) {
 216                         //clear out old files
 217                         ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close();
 218                         ofstream outNames; m->openOutputFile(newNamesFile, outNames);  outNames.close();
 219                         newMapFile = fileroot + "precluster.";
 220
 221                         //parse fasta and name file by group
 222                         SequenceParser* parser;
 223                         if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile);      }
 224                         else                            { parser = new SequenceParser(groupfile, fastafile);                    }
 225
 226                         vector<string> groups = parser->getNamesOfGroups();
 227
 228                         if(processors == 1)     {       driverGroups(parser, newFastaFile, newNamesFile, newMapFile, 0, groups.size(), groups); }
 229                         else                            {       createProcessesGroups(parser, newFastaFile, newNamesFile, newMapFile, groups);                  }
 230
 231                         delete parser;
 232
 233                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        }        return 0; }
 234
 235                         //run unique.seqs for deconvolute results
 236                         string inputString = "fasta=" + newFastaFile;
 237                         if (namefile != "") { inputString += ", name=" + newNamesFile; }
 238                         m->mothurOutEndLine();
 239                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 240                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 241                         m->mothurCalling = true;
 242
 243                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 244                         uniqueCommand->execute();
 245
 246                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 247
 248                         delete uniqueCommand;
 249                         m->mothurCalling = false;
 250                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 251
 252                         m->renameFile(filenames["fasta"][0], newFastaFile);
 253             m->renameFile(filenames["name"][0], newNamesFile);
 254
 255                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine();
 256
 257                 }else {
 258                         if (namefile != "") { readNameFile(); }
 259
 260                         //reads fasta file and return number of seqs
 261                         int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
 262
 263                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 264
 265                         if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0;  }
 266                         if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0;  }
 267
 268                         int count = process(newMapFile);
 269                         outputNames.push_back(newMapFile); outputTypes["map"].push_back(newMapFile);
 270
 271                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 272
 273                         m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 274                         m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 275                         printData(newFastaFile, newNamesFile);
 276
 277                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 278                 }
 279
 280                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 281
 282                 m->mothurOutEndLine();
 283                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 284                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 285                 m->mothurOutEndLine();
 286
 287                 //set fasta file as new current fastafile
 288                 string current = "";
 289                 itTypes = outputTypes.find("fasta");
 290                 if (itTypes != outputTypes.end()) {
 291                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 292                 }
 293
 294                 itTypes = outputTypes.find("name");
 295                 if (itTypes != outputTypes.end()) {
 296                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 297                 }
 298
 299                 return 0;
 300
 301         }
 302         catch(exception& e) {
 303                 m->errorOut(e, "PreClusterCommand", "execute");
 304                 exit(1);
 305         }
 306 }
 307 /**************************************************************************************************/
 308 int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newFName, string newNName, string newMFile, vector<string> groups) {
 309         try {
 310
 311                 vector<int> processIDS;
 312                 int process = 1;
 313                 int num = 0;
 314
 315                 //sanity check
 316                 if (groups.size() < processors) { processors = groups.size(); }
 317
 318                 //divide the groups between the processors
 319                 vector<linePair> lines;
 320                 int numGroupsPerProcessor = groups.size() / processors;
 321                 for (int i = 0; i < processors; i++) {
 322                         int startIndex =  i * numGroupsPerProcessor;
 323                         int endIndex = (i+1) * numGroupsPerProcessor;
 324                         if(i == (processors - 1)){      endIndex = groups.size();       }
 325                         lines.push_back(linePair(startIndex, endIndex));
 326                 }
 327
 328 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 329
 330                 //loop through and create all the processes you want
 331                 while (process != processors) {
 332                         int pid = fork();
 333
 334                         if (pid > 0) {
 335                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 336                                 process++;
 337                         }else if (pid == 0){
 338                 outputNames.clear();
 339                                 num = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
 340
 341                 string tempFile = toString(getpid()) + ".outputNames.temp";
 342                 ofstream outTemp;
 343                 m->openOutputFile(tempFile, outTemp);
 344
 345                 outTemp << outputNames.size();
 346                 for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; }
 347                 outTemp.close();
 348
 349                                 exit(0);
 350                         }else {
 351                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 352                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 353                                 exit(0);
 354                         }
 355                 }
 356
 357                 //do my part
 358                 num = driverGroups(parser, newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
 359
 360                 //force parent to wait until all the processes are done
 361                 for (int i=0;i<processIDS.size();i++) {
 362                         int temp = processIDS[i];
 363                         wait(&temp);
 364                 }
 365
 366         for (int i = 0; i < processIDS.size(); i++) {
 367             string tempFile = toString(processIDS[i]) +  ".outputNames.temp";
 368             ifstream intemp;
 369             m->openInputFile(tempFile, intemp);
 370
 371             int num;
 372             intemp >> num;
 373             for (int k = 0; k < num; k++) {
 374                 string name = "";
 375                 intemp >> name; m->gobble(intemp);
 376
 377                 outputNames.push_back(name); outputTypes["map"].push_back(name);
 378             }
 379             intemp.close();
 380             m->mothurRemove(tempFile);
 381         }
 382 #else
 383
 384                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 385                 //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
 386                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 387                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 388
 389                 vector<preClusterData*> pDataArray;
 390                 DWORD   dwThreadIdArray[processors-1];
 391                 HANDLE  hThreadArray[processors-1];
 392
 393                 //Create processor worker threads.
 394                 for( int i=1; i<processors; i++ ){
 395                         // Allocate memory for thread data.
 396                         string extension = toString(i) + ".temp";
 397
 398                         preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, i);
 399                         pDataArray.push_back(tempPreCluster);
 400                         processIDS.push_back(i);
 401
 402                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 403                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 404                         hThreadArray[i-1] = CreateThread(NULL, 0, MyPreclusterThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 405                 }
 406
 407
 408                 //using the main process as a worker saves time and memory
 409                 num = driverGroups(parser, newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
 410
 411                 //Wait until all threads have terminated.
 412                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 413
 414                 //Close all thread handles and free memory allocations.
 415                 for(int i=0; i < pDataArray.size(); i++){
 416                         for (int j = 0; j < pDataArray[i]->mapFileNames.size(); j++) {
 417                                 outputNames.push_back(pDataArray[i]->mapFileNames[j]); outputTypes["map"].push_back(pDataArray[i]->mapFileNames[j]);
 418                         }
 419                         CloseHandle(hThreadArray[i]);
 420                         delete pDataArray[i];
 421                 }
 422
 423 #endif
 424
 425                 //append output files
 426                 for(int i=0;i<processIDS.size();i++){
 427                         //newFName = m->getFullPathName(".\\" + newFName);
 428                         //newNName = m->getFullPathName(".\\" + newNName);
 429
 430                         m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
 431                         m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
 432
 433                         m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
 434                         m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
 435                 }
 436
 437                 return num;
 438
 439         }
 440         catch(exception& e) {
 441                 m->errorOut(e, "PreClusterCommand", "createProcessesGroups");
 442                 exit(1);
 443         }
 444 }
 445 /**************************************************************************************************/
 446 int PreClusterCommand::driverGroups(SequenceParser* parser, string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
 447         try {
 448
 449                 int numSeqs = 0;
 450
 451                 //precluster each group
 452                 for (int i = start; i < end; i++) {
 453
 454                         start = time(NULL);
 455
 456                         if (m->control_pressed) {  return 0; }
 457
 458                         m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
 459
 460                         map<string, string> thisNameMap;
 461                         if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); }
 462                         vector<Sequence> thisSeqs = parser->getSeqs(groups[i]);
 463
 464                         //fill alignSeqs with this groups info.
 465                         numSeqs = loadSeqs(thisNameMap, thisSeqs);
 466
 467                         if (m->control_pressed) {   return 0; }
 468
 469                         if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); m->control_pressed = true; return 0;  }
 470
 471                         int count = process(newMFile+groups[i]+".map");
 472                         outputNames.push_back(newMFile+groups[i]+".map"); outputTypes["map"].push_back(newMFile+groups[i]+".map");
 473
 474                         if (m->control_pressed) {  return 0; }
 475
 476                         m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 477                         m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 478                         printData(newFFile, newNFile);
 479
 480                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 481
 482                 }
 483
 484                 return numSeqs;
 485         }
 486         catch(exception& e) {
 487                 m->errorOut(e, "PreClusterCommand", "driverGroups");
 488                 exit(1);
 489         }
 490 }
 491 /**************************************************************************************************/
 492 int PreClusterCommand::process(string newMapFile){
 493         try {
 494                 ofstream out;
 495                 m->openOutputFile(newMapFile, out);
 496
 497                 //sort seqs by number of identical seqs
 498                 sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
 499
 500                 int count = 0;
 501                 int numSeqs = alignSeqs.size();
 502
 503                 //think about running through twice...
 504                 for (int i = 0; i < numSeqs; i++) {
 505
 506                         //are you active
 507                         //                      itActive = active.find(alignSeqs[i].seq.getName());
 508
 509                         if (alignSeqs[i].active) {  //this sequence has not been merged yet
 510
 511                                 string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n";
 512
 513                                 //try to merge it with all smaller seqs
 514                                 for (int j = i+1; j < numSeqs; j++) {
 515
 516                                         if (m->control_pressed) { out.close(); return 0; }
 517
 518                                         if (alignSeqs[j].active) {  //this sequence has not been merged yet
 519                                                 //are you within "diff" bases
 520                                                 int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
 521
 522                                                 if (mismatch <= diffs) {
 523                                                         //merge
 524                                                         alignSeqs[i].names += ',' + alignSeqs[j].names;
 525                                                         alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
 526
 527                                                         chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n";
 528
 529                                                         alignSeqs[j].active = 0;
 530                                                         alignSeqs[j].numIdentical = 0;
 531                                                         count++;
 532                                                 }
 533                                         }//end if j active
 534                                 }//end for loop j
 535
 536                                 //remove from active list
 537                                 alignSeqs[i].active = 0;
 538
 539                                 out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;;
 540
 541                         }//end if active i
 542                         if(i % 100 == 0)        { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
 543                 }
 544                 out.close();
 545
 546                 if(numSeqs % 100 != 0)  { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();   }
 547
 548                 return count;
 549
 550         }
 551         catch(exception& e) {
 552                 m->errorOut(e, "PreClusterCommand", "process");
 553                 exit(1);
 554         }
 555 }
 556 /**************************************************************************************************/
 557 int PreClusterCommand::readFASTA(){
 558         try {
 559                 //ifstream inNames;
 560                 ifstream inFasta;
 561
 562                 //m->openInputFile(namefile, inNames);
 563                 m->openInputFile(fastafile, inFasta);
 564
 565                 //string firstCol, secondCol, nameString;
 566                 set<int> lengths;
 567
 568                 while (!inFasta.eof()) {
 569
 570                         if (m->control_pressed) { inFasta.close(); return 0; }
 571
 572                         //inNames >> firstCol >> secondCol;
 573                         //nameString = secondCol;
 574
 575                         //m->gobble(inNames);
 576                         //int size = 1;
 577                         //while (secondCol.find_first_of(',') != -1) {
 578                         //      size++;
 579                         //      secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 580                         //}
 581
 582                         Sequence seq(inFasta);  m->gobble(inFasta);
 583
 584                         if (seq.getName() != "") {  //can get "" if commented line is at end of fasta file
 585                                 if (namefile != "") {
 586                                         itSize = sizes.find(seq.getName());
 587
 588                                         if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
 589                                         else{
 590                                                 seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
 591                                                 alignSeqs.push_back(tempNode);
 592                                                 lengths.insert(seq.getAligned().length());
 593                                         }
 594                                 }else { //no names file, you are identical to yourself
 595                                         seqPNode tempNode(1, seq, seq.getName());
 596                                         alignSeqs.push_back(tempNode);
 597                                         lengths.insert(seq.getAligned().length());
 598                                 }
 599                         }
 600                 }
 601                 inFasta.close();
 602                 //inNames.close();
 603
 604         if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
 605         else if (lengths.size() == 1) { length = *(lengths.begin()); }
 606
 607                 return alignSeqs.size();
 608         }
 609
 610         catch(exception& e) {
 611                 m->errorOut(e, "PreClusterCommand", "readFASTA");
 612                 exit(1);
 613         }
 614 }
 615 /**************************************************************************************************/
 616 int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs){
 617         try {
 618                 set<int> lengths;
 619                 alignSeqs.clear();
 620                 map<string, string>::iterator it;
 621                 bool error = false;
 622
 623                 for (int i = 0; i < thisSeqs.size(); i++) {
 624
 625                         if (m->control_pressed) { return 0; }
 626
 627                         if (namefile != "") {
 628                                 it = thisName.find(thisSeqs[i].getName());
 629
 630                                 //should never be true since parser checks for this
 631                                 if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
 632                                 else{
 633                                         //get number of reps
 634                                         int numReps = 1;
 635                                         for(int j=0;j<(it->second).length();j++){
 636                                                 if((it->second)[j] == ','){     numReps++;      }
 637                                         }
 638
 639                                         seqPNode tempNode(numReps, thisSeqs[i], it->second);
 640                                         alignSeqs.push_back(tempNode);
 641                     lengths.insert(thisSeqs[i].getAligned().length());
 642                                 }
 643                         }else { //no names file, you are identical to yourself
 644                                 seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName());
 645                                 alignSeqs.push_back(tempNode);
 646                                 lengths.insert(thisSeqs[i].getAligned().length());
 647                         }
 648                 }
 649
 650         if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
 651         else if (lengths.size() == 1) { length = *(lengths.begin()); }
 652
 653                 //sanity check
 654                 if (error) { m->control_pressed = true; }
 655
 656                 thisSeqs.clear();
 657
 658                 return alignSeqs.size();
 659         }
 660
 661         catch(exception& e) {
 662                 m->errorOut(e, "PreClusterCommand", "loadSeqs");
 663                 exit(1);
 664         }
 665 }
 666
 667 /**************************************************************************************************/
 668
 669 int PreClusterCommand::calcMisMatches(string seq1, string seq2){
 670         try {
 671                 int numBad = 0;
 672
 673                 for (int i = 0; i < seq1.length(); i++) {
 674                         //do they match
 675                         if (seq1[i] != seq2[i]) { numBad++; }
 676                         if (numBad > diffs) { return length;  } //to far to cluster
 677                 }
 678
 679                 return numBad;
 680         }
 681         catch(exception& e) {
 682                 m->errorOut(e, "PreClusterCommand", "calcMisMatches");
 683                 exit(1);
 684         }
 685 }
 686
 687 /**************************************************************************************************/
 688
 689 void PreClusterCommand::printData(string newfasta, string newname){
 690         try {
 691                 ofstream outFasta;
 692                 ofstream outNames;
 693
 694                 if (bygroup) {
 695                         m->openOutputFileAppend(newfasta, outFasta);
 696                         m->openOutputFileAppend(newname, outNames);
 697                 }else {
 698                         m->openOutputFile(newfasta, outFasta);
 699                         m->openOutputFile(newname, outNames);
 700                 }
 701
 702                 for (int i = 0; i < alignSeqs.size(); i++) {
 703                         if (alignSeqs[i].numIdentical != 0) {
 704                                 alignSeqs[i].seq.printSequence(outFasta);
 705                                 outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
 706                         }
 707                 }
 708
 709                 outFasta.close();
 710                 outNames.close();
 711
 712         }
 713         catch(exception& e) {
 714                 m->errorOut(e, "PreClusterCommand", "printData");
 715                 exit(1);
 716         }
 717 }
 718 /**************************************************************************************************/
 719
 720 void PreClusterCommand::readNameFile(){
 721         try {
 722                 ifstream in;
 723                 m->openInputFile(namefile, in);
 724                 string firstCol, secondCol;
 725
 726                 while (!in.eof()) {
 727                         in >> firstCol >> secondCol; m->gobble(in);
 728                         names[firstCol] = secondCol;
 729                         int size = 1;
 730
 731                         for(int i=0;i<secondCol.size();i++){
 732                                 if(secondCol[i] == ','){        size++; }
 733                         }
 734                         sizes[firstCol] = size;
 735                 }
 736                 in.close();
 737         }
 738         catch(exception& e) {
 739                 m->errorOut(e, "PreClusterCommand", "readNameFile");
 740                 exit(1);
 741         }
 742 }
 743
 744 /**************************************************************************************************/
 745
 746