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","fasta-name",false,true,true); parameters.push_back(pfasta);
  17                 CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
  18         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
  19                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
  20                 CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pdiffs);
  21                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  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, "PreClusterCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string PreClusterCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The pre.cluster command groups sequences that are within a given number of base mismatches.\n";
  39                 helpString += "The pre.cluster command outputs a new fasta and name file.\n";
  40                 helpString += "The pre.cluster command parameters are fasta, name, group, count, processors and diffs. The fasta parameter is required. \n";
  41                 helpString += "The name 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";
  42                 helpString += "The group parameter allows you to provide a group file so you can cluster by group. \n";
  43         helpString += "The count parameter allows you to provide a count file so you can cluster by group. \n";
  44                 helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n";
  45                 helpString += "The pre.cluster command should be in the following format: \n";
  46                 helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n";
  47                 helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n";
  48                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  49                 return helpString;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "PreClusterCommand", "getHelpString");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 string PreClusterCommand::getOutputPattern(string type) {
  58     try {
  59         string pattern = "";
  60
  61         if (type == "fasta") {  pattern = "[filename],precluster,[extension]"; }
  62         else if (type == "name") {  pattern = "[filename],precluster.names"; }
  63         else if (type == "count") {  pattern = "[filename],precluster.count_table"; }
  64         else if (type == "map") {  pattern =  "[filename],precluster.map"; }
  65         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  66
  67         return pattern;
  68     }
  69     catch(exception& e) {
  70         m->errorOut(e, "PreClusterCommand", "getOutputPattern");
  71         exit(1);
  72     }
  73 }
  74 //**********************************************************************************************************************
  75 PreClusterCommand::PreClusterCommand(){
  76         try {
  77                 abort = true; calledHelp = true;
  78                 setParameters();
  79                 vector<string> tempOutNames;
  80                 outputTypes["fasta"] = tempOutNames;
  81                 outputTypes["name"] = tempOutNames;
  82         outputTypes["count"] = tempOutNames;
  83                 outputTypes["map"] = tempOutNames;
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
  87                 exit(1);
  88         }
  89 }
  90 //**********************************************************************************************************************
  91
  92 PreClusterCommand::PreClusterCommand(string option) {
  93         try {
  94                 abort = false; calledHelp = false;
  95
  96                 //allow user to run help
  97                 if(option == "help") { help(); abort = true; calledHelp = true; }
  98                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  99
 100                 else {
 101                         vector<string> myArray = setParameters();
 102
 103                         OptionParser parser(option);
 104                         map<string, string> parameters = parser.getParameters();
 105
 106                         ValidParameters validParameter;
 107                         map<string, string>::iterator it;
 108
 109                         //check to make sure all parameters are valid for command
 110                         for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
 111                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 112                         }
 113
 114                         //initialize outputTypes
 115                         vector<string> tempOutNames;
 116                         outputTypes["fasta"] = tempOutNames;
 117                         outputTypes["name"] = tempOutNames;
 118                         outputTypes["map"] = tempOutNames;
 119             outputTypes["count"] = 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                 it = parameters.find("count");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 156                                 }
 157                         }
 158
 159                         //check for required parameters
 160                         fastafile = validParameter.validFile(parameters, "fasta", true);
 161                         if (fastafile == "not found") {
 162                                 fastafile = m->getFastaFile();
 163                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 164                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 165                         }
 166                         else if (fastafile == "not open") { abort = true; }
 167                         else { m->setFastaFile(fastafile); }
 168
 169                         //if the user changes the output directory command factory will send this info to us in the output parameter
 170                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 171                                 outputDir = "";
 172                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 173                         }
 174
 175                         //check for optional parameter and set defaults
 176                         // ...at some point should added some additional type checking...
 177                         namefile = validParameter.validFile(parameters, "name", true);
 178                         if (namefile == "not found") { namefile =  "";  }
 179                         else if (namefile == "not open") { namefile = ""; abort = true; }
 180                         else {  m->setNameFile(namefile); }
 181
 182                         groupfile = validParameter.validFile(parameters, "group", true);
 183                         if (groupfile == "not found") { groupfile =  "";  bygroup = false; }
 184                         else if (groupfile == "not open") { abort = true; groupfile =  ""; }
 185                         else {   m->setGroupFile(groupfile); bygroup = true;  }
 186
 187             countfile = validParameter.validFile(parameters, "count", true);
 188                         if (countfile == "not found") { countfile =  "";   }
 189                         else if (countfile == "not open") { abort = true; countfile =  ""; }
 190                         else {
 191                 m->setCountTableFile(countfile);
 192                 ct.readTable(countfile);
 193                 if (ct.hasGroupInfo()) { bygroup = true; }
 194                 else { bygroup = false;  }
 195             }
 196
 197             if ((namefile != "") && (countfile != "")) {
 198                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 199             }
 200
 201             if ((groupfile != "") && (countfile != "")) {
 202                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 203             }
 204
 205
 206                         string temp     = validParameter.validFile(parameters, "diffs", false);         if(temp == "not found"){        temp = "1"; }
 207                         m->mothurConvert(temp, diffs);
 208
 209                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 210                         m->setProcessors(temp);
 211                         m->mothurConvert(temp, processors);
 212
 213             if (countfile == "") {
 214                 if (namefile == "") {
 215                     vector<string> files; files.push_back(fastafile);
 216                     parser.getNameFile(files);
 217                 }
 218             }
 219                 }
 220
 221         }
 222         catch(exception& e) {
 223                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
 224                 exit(1);
 225         }
 226 }
 227 //**********************************************************************************************************************
 228
 229 int PreClusterCommand::execute(){
 230         try {
 231
 232                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 233
 234                 int start = time(NULL);
 235
 236                 string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
 237         map<string, string> variables;
 238         variables["[filename]"] = fileroot;
 239                 string newNamesFile = getOutputFileName("name",variables);
 240         string newCountFile = getOutputFileName("count",variables);
 241                 string newMapFile = getOutputFileName("map",variables); //add group name if by group
 242         variables["[extension]"] = m->getExtension(fastafile);
 243                 string newFastaFile = getOutputFileName("fasta", variables);
 244                 outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
 245                 if (countfile == "") { outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile); }
 246                 else { outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile); }
 247
 248                 if (bygroup) {
 249                         //clear out old files
 250                         ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close();
 251                         ofstream outNames; m->openOutputFile(newNamesFile, outNames);  outNames.close();
 252                         newMapFile = fileroot + "precluster.";
 253
 254                         //parse fasta and name file by group
 255             vector<string> groups;
 256                         if (countfile != "") {
 257                 cparser = new SequenceCountParser(countfile, fastafile);
 258                 groups = cparser->getNamesOfGroups();
 259             }else {
 260                 if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile);      }
 261                 else                            { parser = new SequenceParser(groupfile, fastafile);                    }
 262                 groups = parser->getNamesOfGroups();
 263                         }
 264
 265                         if(processors == 1)     {       driverGroups(newFastaFile, newNamesFile, newMapFile, 0, groups.size(), groups); }
 266                         else                            {       createProcessesGroups(newFastaFile, newNamesFile, newMapFile, groups);                  }
 267
 268                         if (countfile != "") {
 269                 mergeGroupCounts(newCountFile, newNamesFile, newFastaFile);
 270                 delete cparser;
 271             }else {
 272                 delete parser;
 273                 //run unique.seqs for deconvolute results
 274                 string inputString = "fasta=" + newFastaFile;
 275                 if (namefile != "") { inputString += ", name=" + newNamesFile; }
 276                 m->mothurOutEndLine();
 277                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 278                 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 279                 m->mothurCalling = true;
 280
 281                 Command* uniqueCommand = new DeconvoluteCommand(inputString);
 282                 uniqueCommand->execute();
 283
 284                 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 285
 286                 delete uniqueCommand;
 287                 m->mothurCalling = false;
 288                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 289
 290                 m->renameFile(filenames["fasta"][0], newFastaFile);
 291                 m->renameFile(filenames["name"][0], newNamesFile);
 292                         }
 293             if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]);        }        return 0; }
 294                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine();
 295
 296                 }else {
 297                         if (namefile != "") { readNameFile(); }
 298
 299                         //reads fasta file and return number of seqs
 300                         int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
 301
 302                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 303
 304                         if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0;  }
 305                         if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0;  }
 306
 307                         int count = process(newMapFile);
 308                         outputNames.push_back(newMapFile); outputTypes["map"].push_back(newMapFile);
 309
 310                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 311
 312                         m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 313                         m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 314                         if (countfile != "") { newNamesFile = newCountFile; }
 315             printData(newFastaFile, newNamesFile, "");
 316
 317                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 318                 }
 319
 320                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 321
 322                 m->mothurOutEndLine();
 323                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 324                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 325                 m->mothurOutEndLine();
 326
 327                 //set fasta file as new current fastafile
 328                 string current = "";
 329                 itTypes = outputTypes.find("fasta");
 330                 if (itTypes != outputTypes.end()) {
 331                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 332                 }
 333
 334                 itTypes = outputTypes.find("name");
 335                 if (itTypes != outputTypes.end()) {
 336                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 337                 }
 338
 339         itTypes = outputTypes.find("count");
 340                 if (itTypes != outputTypes.end()) {
 341                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 342                 }
 343
 344                 return 0;
 345
 346         }
 347         catch(exception& e) {
 348                 m->errorOut(e, "PreClusterCommand", "execute");
 349                 exit(1);
 350         }
 351 }
 352 /**************************************************************************************************/
 353 int PreClusterCommand::createProcessesGroups(string newFName, string newNName, string newMFile, vector<string> groups) {
 354         try {
 355
 356                 vector<int> processIDS;
 357                 int process = 1;
 358                 int num = 0;
 359
 360                 //sanity check
 361                 if (groups.size() < processors) { processors = groups.size(); }
 362
 363                 //divide the groups between the processors
 364                 vector<linePair> lines;
 365                 int numGroupsPerProcessor = groups.size() / processors;
 366                 for (int i = 0; i < processors; i++) {
 367                         int startIndex =  i * numGroupsPerProcessor;
 368                         int endIndex = (i+1) * numGroupsPerProcessor;
 369                         if(i == (processors - 1)){      endIndex = groups.size();       }
 370                         lines.push_back(linePair(startIndex, endIndex));
 371                 }
 372
 373 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 374
 375                 //loop through and create all the processes you want
 376                 while (process != processors) {
 377                         int pid = fork();
 378
 379                         if (pid > 0) {
 380                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 381                                 process++;
 382                         }else if (pid == 0){
 383                 outputNames.clear();
 384                                 num = driverGroups(newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
 385
 386                 string tempFile = toString(getpid()) + ".outputNames.temp";
 387                 ofstream outTemp;
 388                 m->openOutputFile(tempFile, outTemp);
 389
 390                 outTemp << outputNames.size();
 391                 for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; }
 392                 outTemp.close();
 393
 394                                 exit(0);
 395                         }else {
 396                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 397                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 398                                 exit(0);
 399                         }
 400                 }
 401
 402                 //do my part
 403                 num = driverGroups(newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
 404
 405                 //force parent to wait until all the processes are done
 406                 for (int i=0;i<processIDS.size();i++) {
 407                         int temp = processIDS[i];
 408                         wait(&temp);
 409                 }
 410
 411         for (int i = 0; i < processIDS.size(); i++) {
 412             string tempFile = toString(processIDS[i]) +  ".outputNames.temp";
 413             ifstream intemp;
 414             m->openInputFile(tempFile, intemp);
 415
 416             int num;
 417             intemp >> num;
 418             for (int k = 0; k < num; k++) {
 419                 string name = "";
 420                 intemp >> name; m->gobble(intemp);
 421
 422                 outputNames.push_back(name); outputTypes["map"].push_back(name);
 423             }
 424             intemp.close();
 425             m->mothurRemove(tempFile);
 426         }
 427 #else
 428
 429                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 430                 //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
 431                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 432                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 433
 434                 vector<preClusterData*> pDataArray;
 435                 DWORD   dwThreadIdArray[processors-1];
 436                 HANDLE  hThreadArray[processors-1];
 437
 438                 //Create processor worker threads.
 439                 for( int i=1; i<processors; i++ ){
 440                         // Allocate memory for thread data.
 441                         string extension = toString(i) + ".temp";
 442
 443                         preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, countfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, i);
 444                         pDataArray.push_back(tempPreCluster);
 445                         processIDS.push_back(i);
 446
 447                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 448                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 449                         hThreadArray[i-1] = CreateThread(NULL, 0, MyPreclusterThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 450                 }
 451
 452
 453                 //using the main process as a worker saves time and memory
 454                 num = driverGroups(newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
 455
 456                 //Wait until all threads have terminated.
 457                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 458
 459                 //Close all thread handles and free memory allocations.
 460                 for(int i=0; i < pDataArray.size(); i++){
 461                         for (int j = 0; j < pDataArray[i]->mapFileNames.size(); j++) {
 462                                 outputNames.push_back(pDataArray[i]->mapFileNames[j]); outputTypes["map"].push_back(pDataArray[i]->mapFileNames[j]);
 463                         }
 464                         CloseHandle(hThreadArray[i]);
 465                         delete pDataArray[i];
 466                 }
 467
 468 #endif
 469
 470                 //append output files
 471                 for(int i=0;i<processIDS.size();i++){
 472                         //newFName = m->getFullPathName(".\\" + newFName);
 473                         //newNName = m->getFullPathName(".\\" + newNName);
 474
 475                         m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
 476                         m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
 477
 478                         m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
 479                         m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
 480                 }
 481
 482                 return num;
 483
 484         }
 485         catch(exception& e) {
 486                 m->errorOut(e, "PreClusterCommand", "createProcessesGroups");
 487                 exit(1);
 488         }
 489 }
 490 /**************************************************************************************************/
 491 int PreClusterCommand::driverGroups(string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
 492         try {
 493
 494                 int numSeqs = 0;
 495
 496                 //precluster each group
 497                 for (int i = start; i < end; i++) {
 498
 499                         start = time(NULL);
 500
 501                         if (m->control_pressed) {  return 0; }
 502
 503                         m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
 504
 505                         map<string, string> thisNameMap;
 506             vector<Sequence> thisSeqs;
 507                         if (groupfile != "") {
 508                 thisSeqs = parser->getSeqs(groups[i]);
 509             }else if (countfile != "") {
 510                 thisSeqs = cparser->getSeqs(groups[i]);
 511             }
 512                         if (namefile != "") {  thisNameMap = parser->getNameMap(groups[i]); }
 513
 514                         //fill alignSeqs with this groups info.
 515                         numSeqs = loadSeqs(thisNameMap, thisSeqs, groups[i]);
 516
 517                         if (m->control_pressed) {   return 0; }
 518
 519                         if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); m->control_pressed = true; return 0;  }
 520
 521                         int count= process(newMFile+groups[i]+".map");
 522                         outputNames.push_back(newMFile+groups[i]+".map"); outputTypes["map"].push_back(newMFile+groups[i]+".map");
 523
 524                         if (m->control_pressed) {  return 0; }
 525
 526                         m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 527                         m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 528                         printData(newFFile, newNFile, groups[i]);
 529
 530                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 531
 532                 }
 533
 534                 return numSeqs;
 535         }
 536         catch(exception& e) {
 537                 m->errorOut(e, "PreClusterCommand", "driverGroups");
 538                 exit(1);
 539         }
 540 }
 541 /**************************************************************************************************/
 542 int PreClusterCommand::process(string newMapFile){
 543         try {
 544                 ofstream out;
 545                 m->openOutputFile(newMapFile, out);
 546
 547                 //sort seqs by number of identical seqs
 548                 sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
 549
 550                 int count = 0;
 551                 int numSeqs = alignSeqs.size();
 552
 553                 //think about running through twice...
 554                 for (int i = 0; i < numSeqs; i++) {
 555
 556                         //are you active
 557                         //                      itActive = active.find(alignSeqs[i].seq.getName());
 558
 559                         if (alignSeqs[i].active) {  //this sequence has not been merged yet
 560
 561                                 string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n";
 562
 563                                 //try to merge it with all smaller seqs
 564                                 for (int j = i+1; j < numSeqs; j++) {
 565
 566                                         if (m->control_pressed) { out.close(); return 0; }
 567
 568                                         if (alignSeqs[j].active) {  //this sequence has not been merged yet
 569                                                 //are you within "diff" bases
 570                                                 int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
 571
 572                                                 if (mismatch <= diffs) {
 573                                                         //merge
 574                                                         alignSeqs[i].names += ',' + alignSeqs[j].names;
 575                                                         alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
 576
 577                                                         chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n";
 578
 579                                                         alignSeqs[j].active = 0;
 580                                                         alignSeqs[j].numIdentical = 0;
 581                                                         count++;
 582                                                 }
 583                                         }//end if j active
 584                                 }//end for loop j
 585
 586                                 //remove from active list
 587                                 alignSeqs[i].active = 0;
 588
 589                                 out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;;
 590
 591                         }//end if active i
 592                         if(i % 100 == 0)        { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
 593                 }
 594                 out.close();
 595
 596                 if(numSeqs % 100 != 0)  { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();   }
 597
 598                 return count;
 599
 600         }
 601         catch(exception& e) {
 602                 m->errorOut(e, "PreClusterCommand", "process");
 603                 exit(1);
 604         }
 605 }
 606 /**************************************************************************************************/
 607 int PreClusterCommand::readFASTA(){
 608         try {
 609                 //ifstream inNames;
 610                 ifstream inFasta;
 611
 612                 m->openInputFile(fastafile, inFasta);
 613                 set<int> lengths;
 614
 615                 while (!inFasta.eof()) {
 616
 617                         if (m->control_pressed) { inFasta.close(); return 0; }
 618
 619                         Sequence seq(inFasta);  m->gobble(inFasta);
 620
 621                         if (seq.getName() != "") {  //can get "" if commented line is at end of fasta file
 622                                 if (namefile != "") {
 623                                         itSize = sizes.find(seq.getName());
 624
 625                                         if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
 626                                         else{
 627                                                 seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
 628                                                 alignSeqs.push_back(tempNode);
 629                                                 lengths.insert(seq.getAligned().length());
 630                                         }
 631                                 }else { //no names file, you are identical to yourself
 632                     int numRep = 1;
 633                     if (countfile != "") { numRep = ct.getNumSeqs(seq.getName()); }
 634                                         seqPNode tempNode(numRep, seq, seq.getName());
 635                                         alignSeqs.push_back(tempNode);
 636                                         lengths.insert(seq.getAligned().length());
 637                                 }
 638                         }
 639                 }
 640                 inFasta.close();
 641
 642         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(); }
 643         else if (lengths.size() == 1) { length = *(lengths.begin()); }
 644
 645                 return alignSeqs.size();
 646         }
 647
 648         catch(exception& e) {
 649                 m->errorOut(e, "PreClusterCommand", "readFASTA");
 650                 exit(1);
 651         }
 652 }
 653 /**************************************************************************************************/
 654 int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs, string group){
 655         try {
 656                 set<int> lengths;
 657                 alignSeqs.clear();
 658                 map<string, string>::iterator it;
 659                 bool error = false;
 660         map<string, int> thisCount;
 661         if (countfile != "") { thisCount = cparser->getCountTable(group);  }
 662
 663                 for (int i = 0; i < thisSeqs.size(); i++) {
 664
 665                         if (m->control_pressed) { return 0; }
 666
 667                         if (namefile != "") {
 668                                 it = thisName.find(thisSeqs[i].getName());
 669
 670                                 //should never be true since parser checks for this
 671                                 if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
 672                                 else{
 673                                         //get number of reps
 674                                         int numReps = 1;
 675                                         for(int j=0;j<(it->second).length();j++){
 676                                                 if((it->second)[j] == ','){     numReps++;      }
 677                                         }
 678
 679                                         seqPNode tempNode(numReps, thisSeqs[i], it->second);
 680                                         alignSeqs.push_back(tempNode);
 681                     lengths.insert(thisSeqs[i].getAligned().length());
 682                                 }
 683                         }else { //no names file, you are identical to yourself
 684                 int numRep = 1;
 685                 if (countfile != "") {
 686                     map<string, int>::iterator it2 = thisCount.find(thisSeqs[i].getName());
 687
 688                     //should never be true since parser checks for this
 689                     if (it2 == thisCount.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); error = true; }
 690                     else { numRep = it2->second;  }
 691                 }
 692                                 seqPNode tempNode(numRep, thisSeqs[i], thisSeqs[i].getName());
 693                                 alignSeqs.push_back(tempNode);
 694                                 lengths.insert(thisSeqs[i].getAligned().length());
 695                         }
 696                 }
 697
 698         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(); }
 699         else if (lengths.size() == 1) { length = *(lengths.begin()); }
 700
 701                 //sanity check
 702                 if (error) { m->control_pressed = true; }
 703
 704                 thisSeqs.clear();
 705
 706                 return alignSeqs.size();
 707         }
 708
 709         catch(exception& e) {
 710                 m->errorOut(e, "PreClusterCommand", "loadSeqs");
 711                 exit(1);
 712         }
 713 }
 714
 715 /**************************************************************************************************/
 716
 717 int PreClusterCommand::calcMisMatches(string seq1, string seq2){
 718         try {
 719                 int numBad = 0;
 720
 721                 for (int i = 0; i < seq1.length(); i++) {
 722                         //do they match
 723                         if (seq1[i] != seq2[i]) { numBad++; }
 724                         if (numBad > diffs) { return length;  } //to far to cluster
 725                 }
 726
 727                 return numBad;
 728         }
 729         catch(exception& e) {
 730                 m->errorOut(e, "PreClusterCommand", "calcMisMatches");
 731                 exit(1);
 732         }
 733 }
 734 /**************************************************************************************************/
 735
 736 int PreClusterCommand::mergeGroupCounts(string newcount, string newname, string newfasta){
 737         try {
 738                 ifstream inNames;
 739         m->openInputFile(newname, inNames);
 740
 741         string group, first, second;
 742         set<string> uniqueNames;
 743         while (!inNames.eof()) {
 744             if (m->control_pressed) { break; }
 745             inNames >> group; m->gobble(inNames);
 746             inNames >> first; m->gobble(inNames);
 747             inNames >> second; m->gobble(inNames);
 748
 749             vector<string> names;
 750             m->splitAtComma(second, names);
 751
 752             uniqueNames.insert(first);
 753
 754             int total = ct.getGroupCount(first, group);
 755             for (int i = 1; i < names.size(); i++) {
 756                 total += ct.getGroupCount(names[i], group);
 757                 ct.setAbund(names[i], group, 0);
 758             }
 759             ct.setAbund(first, group, total);
 760         }
 761         inNames.close();
 762
 763         vector<string> namesOfSeqs = ct.getNamesOfSeqs();
 764         for (int i = 0; i < namesOfSeqs.size(); i++) {
 765             if (ct.getNumSeqs(namesOfSeqs[i]) == 0) {
 766                 ct.remove(namesOfSeqs[i]);
 767             }
 768         }
 769
 770         ct.printTable(newcount);
 771         m->mothurRemove(newname);
 772
 773         if (bygroup) { //if by group, must remove the duplicate seqs that are named the same
 774             ifstream in;
 775             m->openInputFile(newfasta, in);
 776
 777             ofstream out;
 778             m->openOutputFile(newfasta+"temp", out);
 779
 780             int count = 0;
 781             set<string> already;
 782             while(!in.eof()) {
 783                 if (m->control_pressed) { break; }
 784
 785                 Sequence seq(in); m->gobble(in);
 786
 787                 if (seq.getName() != "") {
 788                     count++;
 789                     if (already.count(seq.getName()) == 0) {
 790                         seq.printSequence(out);
 791                         already.insert(seq.getName());
 792                     }
 793                 }
 794             }
 795             in.close();
 796             out.close();
 797             m->mothurRemove(newfasta);
 798             m->renameFile(newfasta+"temp", newfasta);
 799         }
 800                         return 0;
 801
 802         }
 803         catch(exception& e) {
 804                 m->errorOut(e, "PreClusterCommand", "mergeGroupCounts");
 805                 exit(1);
 806         }
 807 }
 808
 809 /**************************************************************************************************/
 810
 811 void PreClusterCommand::printData(string newfasta, string newname, string group){
 812         try {
 813                 ofstream outFasta;
 814                 ofstream outNames;
 815
 816                 if (bygroup) {
 817                         m->openOutputFileAppend(newfasta, outFasta);
 818                         m->openOutputFileAppend(newname, outNames);
 819                 }else {
 820                         m->openOutputFile(newfasta, outFasta);
 821                         m->openOutputFile(newname, outNames);
 822                 }
 823
 824         if ((countfile != "") && (group == ""))  { outNames << "Representative_Sequence\ttotal\n";  }
 825                 for (int i = 0; i < alignSeqs.size(); i++) {
 826                         if (alignSeqs[i].numIdentical != 0) {
 827                                 alignSeqs[i].seq.printSequence(outFasta);
 828                                 if (countfile != "") {
 829                     if (group != "") {  outNames << group << '\t' << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; }
 830                     else {  outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].numIdentical << endl;  }
 831                 }else {  outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;  }
 832                         }
 833                 }
 834
 835                 outFasta.close();
 836                 outNames.close();
 837
 838         }
 839         catch(exception& e) {
 840                 m->errorOut(e, "PreClusterCommand", "printData");
 841                 exit(1);
 842         }
 843 }
 844 /**************************************************************************************************/
 845
 846 void PreClusterCommand::readNameFile(){
 847         try {
 848                 ifstream in;
 849                 m->openInputFile(namefile, in);
 850                 string firstCol, secondCol;
 851
 852                 while (!in.eof()) {
 853                         in >> firstCol >> secondCol; m->gobble(in);
 854                         names[firstCol] = secondCol;
 855                         int size = 1;
 856
 857                         for(int i=0;i<secondCol.size();i++){
 858                                 if(secondCol[i] == ','){        size++; }
 859                         }
 860                         sizes[firstCol] = size;
 861                 }
 862                 in.close();
 863         }
 864         catch(exception& e) {
 865                 m->errorOut(e, "PreClusterCommand", "readNameFile");
 866                 exit(1);
 867         }
 868 }
 869
 870 /**************************************************************************************************/
 871
 872