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", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
  18         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
  19                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
  20                 CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
  21                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); 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::getOutputFileNameTag(string type, string inputName=""){
  58         try {
  59         string outputFileName = "";
  60                 map<string, vector<string> >::iterator it;
  61
  62         //is this a type this command creates
  63         it = outputTypes.find(type);
  64         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  65         else {
  66             if (type == "fasta") {  outputFileName =  "precluster" + m->getExtension(inputName); }
  67             else if (type == "name") {  outputFileName =  "precluster.names"; }
  68             else if (type == "count") {  outputFileName =  "precluster.count_table"; }
  69             else if (type == "map") {  outputFileName =  "precluster.map"; }
  70             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  71         }
  72         return outputFileName;
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "PreClusterCommand", "getOutputFileNameTag");
  76                 exit(1);
  77         }
  78 }
  79 //**********************************************************************************************************************
  80 PreClusterCommand::PreClusterCommand(){
  81         try {
  82                 abort = true; calledHelp = true;
  83                 setParameters();
  84                 vector<string> tempOutNames;
  85                 outputTypes["fasta"] = tempOutNames;
  86                 outputTypes["name"] = tempOutNames;
  87         outputTypes["count"] = tempOutNames;
  88                 outputTypes["map"] = tempOutNames;
  89         }
  90         catch(exception& e) {
  91                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
  92                 exit(1);
  93         }
  94 }
  95 //**********************************************************************************************************************
  96
  97 PreClusterCommand::PreClusterCommand(string option) {
  98         try {
  99                 abort = false; calledHelp = false;
 100
 101                 //allow user to run help
 102                 if(option == "help") { help(); abort = true; calledHelp = true; }
 103                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 104
 105                 else {
 106                         vector<string> myArray = setParameters();
 107
 108                         OptionParser parser(option);
 109                         map<string, string> parameters = parser.getParameters();
 110
 111                         ValidParameters validParameter;
 112                         map<string, string>::iterator it;
 113
 114                         //check to make sure all parameters are valid for command
 115                         for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
 116                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 117                         }
 118
 119                         //initialize outputTypes
 120                         vector<string> tempOutNames;
 121                         outputTypes["fasta"] = tempOutNames;
 122                         outputTypes["name"] = tempOutNames;
 123                         outputTypes["map"] = tempOutNames;
 124             outputTypes["count"] = tempOutNames;
 125
 126                         //if the user changes the input directory command factory will send this info to us in the output parameter
 127                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 128                         if (inputDir == "not found"){   inputDir = "";          }
 129                         else {
 130                                 string path;
 131                                 it = parameters.find("fasta");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 137                                 }
 138
 139                                 it = parameters.find("name");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 145                                 }
 146
 147                                 it = parameters.find("group");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 153                                 }
 154
 155                 it = parameters.find("count");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 161                                 }
 162                         }
 163
 164                         //check for required parameters
 165                         fastafile = validParameter.validFile(parameters, "fasta", true);
 166                         if (fastafile == "not found") {
 167                                 fastafile = m->getFastaFile();
 168                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 169                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 170                         }
 171                         else if (fastafile == "not open") { abort = true; }
 172                         else { m->setFastaFile(fastafile); }
 173
 174                         //if the user changes the output directory command factory will send this info to us in the output parameter
 175                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 176                                 outputDir = "";
 177                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 178                         }
 179
 180                         //check for optional parameter and set defaults
 181                         // ...at some point should added some additional type checking...
 182                         namefile = validParameter.validFile(parameters, "name", true);
 183                         if (namefile == "not found") { namefile =  "";  }
 184                         else if (namefile == "not open") { namefile = ""; abort = true; }
 185                         else {  m->setNameFile(namefile); }
 186
 187                         groupfile = validParameter.validFile(parameters, "group", true);
 188                         if (groupfile == "not found") { groupfile =  "";  bygroup = false; }
 189                         else if (groupfile == "not open") { abort = true; groupfile =  ""; }
 190                         else {   m->setGroupFile(groupfile); bygroup = true;  }
 191
 192             countfile = validParameter.validFile(parameters, "count", true);
 193                         if (countfile == "not found") { countfile =  "";   }
 194                         else if (countfile == "not open") { abort = true; countfile =  ""; }
 195                         else {
 196                 m->setCountTableFile(countfile);
 197                 ct.readTable(countfile);
 198                 if (ct.hasGroupInfo()) { bygroup = true; }
 199                 else { bygroup = false;  }
 200             }
 201
 202             if ((namefile != "") && (countfile != "")) {
 203                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 204             }
 205
 206             if ((groupfile != "") && (countfile != "")) {
 207                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 208             }
 209
 210
 211                         string temp     = validParameter.validFile(parameters, "diffs", false);         if(temp == "not found"){        temp = "1"; }
 212                         m->mothurConvert(temp, diffs);
 213
 214                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 215                         m->setProcessors(temp);
 216                         m->mothurConvert(temp, processors);
 217
 218             if (countfile == "") {
 219                 if (namefile == "") {
 220                     vector<string> files; files.push_back(fastafile);
 221                     parser.getNameFile(files);
 222                 }
 223             }
 224                 }
 225
 226         }
 227         catch(exception& e) {
 228                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
 229                 exit(1);
 230         }
 231 }
 232 //**********************************************************************************************************************
 233
 234 int PreClusterCommand::execute(){
 235         try {
 236
 237                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 238
 239                 int start = time(NULL);
 240
 241                 string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
 242                 string newFastaFile = fileroot + getOutputFileNameTag("fasta", fastafile);
 243                 string newNamesFile = fileroot + getOutputFileNameTag("name");
 244         string newCountFile = fileroot + getOutputFileNameTag("count");
 245                 string newMapFile = fileroot + getOutputFileNameTag("map"); //add group name if by group
 246                 outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
 247                 if (countfile == "") { outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile); }
 248                 else { outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile); }
 249
 250                 if (bygroup) {
 251                         //clear out old files
 252                         ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close();
 253                         ofstream outNames; m->openOutputFile(newNamesFile, outNames);  outNames.close();
 254                         newMapFile = fileroot + "precluster.";
 255
 256                         //parse fasta and name file by group
 257             vector<string> groups;
 258                         if (countfile != "") {
 259                 cparser = new SequenceCountParser(countfile, fastafile);
 260                 groups = cparser->getNamesOfGroups();
 261             }else {
 262                 if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile);      }
 263                 else                            { parser = new SequenceParser(groupfile, fastafile);                    }
 264                 groups = parser->getNamesOfGroups();
 265                         }
 266
 267                         if(processors == 1)     {       driverGroups(newFastaFile, newNamesFile, newMapFile, 0, groups.size(), groups); }
 268                         else                            {       createProcessesGroups(newFastaFile, newNamesFile, newMapFile, groups);                  }
 269
 270                         if (countfile != "") {
 271                 mergeGroupCounts(newCountFile, newNamesFile, newFastaFile);
 272                 delete cparser;
 273             }else {
 274                 delete parser;
 275                 //run unique.seqs for deconvolute results
 276                 string inputString = "fasta=" + newFastaFile;
 277                 if (namefile != "") { inputString += ", name=" + newNamesFile; }
 278                 m->mothurOutEndLine();
 279                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 280                 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 281                 m->mothurCalling = true;
 282
 283                 Command* uniqueCommand = new DeconvoluteCommand(inputString);
 284                 uniqueCommand->execute();
 285
 286                 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 287
 288                 delete uniqueCommand;
 289                 m->mothurCalling = false;
 290                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 291
 292                 m->renameFile(filenames["fasta"][0], newFastaFile);
 293                 m->renameFile(filenames["name"][0], newNamesFile);
 294                         }
 295             if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]);        }        return 0; }
 296                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine();
 297
 298                 }else {
 299                         if (namefile != "") { readNameFile(); }
 300
 301                         //reads fasta file and return number of seqs
 302                         int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
 303
 304                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 305
 306                         if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0;  }
 307                         if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0;  }
 308
 309                         int count = process(newMapFile);
 310                         outputNames.push_back(newMapFile); outputTypes["map"].push_back(newMapFile);
 311
 312                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 313
 314                         m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 315                         m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 316                         if (countfile != "") { newNamesFile = newCountFile; }
 317             printData(newFastaFile, newNamesFile, "");
 318
 319                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 320                 }
 321
 322                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 323
 324                 m->mothurOutEndLine();
 325                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 326                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 327                 m->mothurOutEndLine();
 328
 329                 //set fasta file as new current fastafile
 330                 string current = "";
 331                 itTypes = outputTypes.find("fasta");
 332                 if (itTypes != outputTypes.end()) {
 333                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 334                 }
 335
 336                 itTypes = outputTypes.find("name");
 337                 if (itTypes != outputTypes.end()) {
 338                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 339                 }
 340
 341         itTypes = outputTypes.find("count");
 342                 if (itTypes != outputTypes.end()) {
 343                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 344                 }
 345
 346                 return 0;
 347
 348         }
 349         catch(exception& e) {
 350                 m->errorOut(e, "PreClusterCommand", "execute");
 351                 exit(1);
 352         }
 353 }
 354 /**************************************************************************************************/
 355 int PreClusterCommand::createProcessesGroups(string newFName, string newNName, string newMFile, vector<string> groups) {
 356         try {
 357
 358                 vector<int> processIDS;
 359                 int process = 1;
 360                 int num = 0;
 361
 362                 //sanity check
 363                 if (groups.size() < processors) { processors = groups.size(); }
 364
 365                 //divide the groups between the processors
 366                 vector<linePair> lines;
 367                 int numGroupsPerProcessor = groups.size() / processors;
 368                 for (int i = 0; i < processors; i++) {
 369                         int startIndex =  i * numGroupsPerProcessor;
 370                         int endIndex = (i+1) * numGroupsPerProcessor;
 371                         if(i == (processors - 1)){      endIndex = groups.size();       }
 372                         lines.push_back(linePair(startIndex, endIndex));
 373                 }
 374
 375 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 376
 377                 //loop through and create all the processes you want
 378                 while (process != processors) {
 379                         int pid = fork();
 380
 381                         if (pid > 0) {
 382                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 383                                 process++;
 384                         }else if (pid == 0){
 385                 outputNames.clear();
 386                                 num = driverGroups(newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
 387
 388                 string tempFile = toString(getpid()) + ".outputNames.temp";
 389                 ofstream outTemp;
 390                 m->openOutputFile(tempFile, outTemp);
 391
 392                 outTemp << outputNames.size();
 393                 for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; }
 394                 outTemp.close();
 395
 396                                 exit(0);
 397                         }else {
 398                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 399                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 400                                 exit(0);
 401                         }
 402                 }
 403
 404                 //do my part
 405                 num = driverGroups(newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
 406
 407                 //force parent to wait until all the processes are done
 408                 for (int i=0;i<processIDS.size();i++) {
 409                         int temp = processIDS[i];
 410                         wait(&temp);
 411                 }
 412
 413         for (int i = 0; i < processIDS.size(); i++) {
 414             string tempFile = toString(processIDS[i]) +  ".outputNames.temp";
 415             ifstream intemp;
 416             m->openInputFile(tempFile, intemp);
 417
 418             int num;
 419             intemp >> num;
 420             for (int k = 0; k < num; k++) {
 421                 string name = "";
 422                 intemp >> name; m->gobble(intemp);
 423
 424                 outputNames.push_back(name); outputTypes["map"].push_back(name);
 425             }
 426             intemp.close();
 427             m->mothurRemove(tempFile);
 428         }
 429 #else
 430
 431                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 432                 //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
 433                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 434                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 435
 436                 vector<preClusterData*> pDataArray;
 437                 DWORD   dwThreadIdArray[processors-1];
 438                 HANDLE  hThreadArray[processors-1];
 439
 440                 //Create processor worker threads.
 441                 for( int i=1; i<processors; i++ ){
 442                         // Allocate memory for thread data.
 443                         string extension = toString(i) + ".temp";
 444
 445                         preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, countfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, i);
 446                         pDataArray.push_back(tempPreCluster);
 447                         processIDS.push_back(i);
 448
 449                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 450                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 451                         hThreadArray[i-1] = CreateThread(NULL, 0, MyPreclusterThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 452                 }
 453
 454
 455                 //using the main process as a worker saves time and memory
 456                 num = driverGroups(newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
 457
 458                 //Wait until all threads have terminated.
 459                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 460
 461                 //Close all thread handles and free memory allocations.
 462                 for(int i=0; i < pDataArray.size(); i++){
 463                         for (int j = 0; j < pDataArray[i]->mapFileNames.size(); j++) {
 464                                 outputNames.push_back(pDataArray[i]->mapFileNames[j]); outputTypes["map"].push_back(pDataArray[i]->mapFileNames[j]);
 465                         }
 466                         CloseHandle(hThreadArray[i]);
 467                         delete pDataArray[i];
 468                 }
 469
 470 #endif
 471
 472                 //append output files
 473                 for(int i=0;i<processIDS.size();i++){
 474                         //newFName = m->getFullPathName(".\\" + newFName);
 475                         //newNName = m->getFullPathName(".\\" + newNName);
 476
 477                         m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
 478                         m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
 479
 480                         m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
 481                         m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
 482                 }
 483
 484                 return num;
 485
 486         }
 487         catch(exception& e) {
 488                 m->errorOut(e, "PreClusterCommand", "createProcessesGroups");
 489                 exit(1);
 490         }
 491 }
 492 /**************************************************************************************************/
 493 int PreClusterCommand::driverGroups(string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
 494         try {
 495
 496                 int numSeqs = 0;
 497
 498                 //precluster each group
 499                 for (int i = start; i < end; i++) {
 500
 501                         start = time(NULL);
 502
 503                         if (m->control_pressed) {  return 0; }
 504
 505                         m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
 506
 507                         map<string, string> thisNameMap;
 508             vector<Sequence> thisSeqs;
 509                         if (groupfile != "") {
 510                 thisSeqs = parser->getSeqs(groups[i]);
 511             }else if (countfile != "") {
 512                 thisSeqs = cparser->getSeqs(groups[i]);
 513             }
 514                         if (namefile != "") {  thisNameMap = parser->getNameMap(groups[i]); }
 515
 516                         //fill alignSeqs with this groups info.
 517                         numSeqs = loadSeqs(thisNameMap, thisSeqs, groups[i]);
 518
 519                         if (m->control_pressed) {   return 0; }
 520
 521                         if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); m->control_pressed = true; return 0;  }
 522
 523                         int count= process(newMFile+groups[i]+".map");
 524                         outputNames.push_back(newMFile+groups[i]+".map"); outputTypes["map"].push_back(newMFile+groups[i]+".map");
 525
 526                         if (m->control_pressed) {  return 0; }
 527
 528                         m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 529                         m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 530                         printData(newFFile, newNFile, groups[i]);
 531
 532                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 533
 534                 }
 535
 536                 return numSeqs;
 537         }
 538         catch(exception& e) {
 539                 m->errorOut(e, "PreClusterCommand", "driverGroups");
 540                 exit(1);
 541         }
 542 }
 543 /**************************************************************************************************/
 544 int PreClusterCommand::process(string newMapFile){
 545         try {
 546                 ofstream out;
 547                 m->openOutputFile(newMapFile, out);
 548
 549                 //sort seqs by number of identical seqs
 550                 sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
 551
 552                 int count = 0;
 553                 int numSeqs = alignSeqs.size();
 554
 555                 //think about running through twice...
 556                 for (int i = 0; i < numSeqs; i++) {
 557
 558                         //are you active
 559                         //                      itActive = active.find(alignSeqs[i].seq.getName());
 560
 561                         if (alignSeqs[i].active) {  //this sequence has not been merged yet
 562
 563                                 string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n";
 564
 565                                 //try to merge it with all smaller seqs
 566                                 for (int j = i+1; j < numSeqs; j++) {
 567
 568                                         if (m->control_pressed) { out.close(); return 0; }
 569
 570                                         if (alignSeqs[j].active) {  //this sequence has not been merged yet
 571                                                 //are you within "diff" bases
 572                                                 int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
 573
 574                                                 if (mismatch <= diffs) {
 575                                                         //merge
 576                                                         alignSeqs[i].names += ',' + alignSeqs[j].names;
 577                                                         alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
 578
 579                                                         chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n";
 580
 581                                                         alignSeqs[j].active = 0;
 582                                                         alignSeqs[j].numIdentical = 0;
 583                                                         count++;
 584                                                 }
 585                                         }//end if j active
 586                                 }//end for loop j
 587
 588                                 //remove from active list
 589                                 alignSeqs[i].active = 0;
 590
 591                                 out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;;
 592
 593                         }//end if active i
 594                         if(i % 100 == 0)        { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
 595                 }
 596                 out.close();
 597
 598                 if(numSeqs % 100 != 0)  { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();   }
 599
 600                 return count;
 601
 602         }
 603         catch(exception& e) {
 604                 m->errorOut(e, "PreClusterCommand", "process");
 605                 exit(1);
 606         }
 607 }
 608 /**************************************************************************************************/
 609 int PreClusterCommand::readFASTA(){
 610         try {
 611                 //ifstream inNames;
 612                 ifstream inFasta;
 613
 614                 m->openInputFile(fastafile, inFasta);
 615                 set<int> lengths;
 616
 617                 while (!inFasta.eof()) {
 618
 619                         if (m->control_pressed) { inFasta.close(); return 0; }
 620
 621                         Sequence seq(inFasta);  m->gobble(inFasta);
 622
 623                         if (seq.getName() != "") {  //can get "" if commented line is at end of fasta file
 624                                 if (namefile != "") {
 625                                         itSize = sizes.find(seq.getName());
 626
 627                                         if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
 628                                         else{
 629                                                 seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
 630                                                 alignSeqs.push_back(tempNode);
 631                                                 lengths.insert(seq.getAligned().length());
 632                                         }
 633                                 }else { //no names file, you are identical to yourself
 634                     int numRep = 1;
 635                     if (countfile != "") { numRep = ct.getNumSeqs(seq.getName()); }
 636                                         seqPNode tempNode(numRep, seq, seq.getName());
 637                                         alignSeqs.push_back(tempNode);
 638                                         lengths.insert(seq.getAligned().length());
 639                                 }
 640                         }
 641                 }
 642                 inFasta.close();
 643
 644         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(); }
 645         else if (lengths.size() == 1) { length = *(lengths.begin()); }
 646
 647                 return alignSeqs.size();
 648         }
 649
 650         catch(exception& e) {
 651                 m->errorOut(e, "PreClusterCommand", "readFASTA");
 652                 exit(1);
 653         }
 654 }
 655 /**************************************************************************************************/
 656 int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs, string group){
 657         try {
 658                 set<int> lengths;
 659                 alignSeqs.clear();
 660                 map<string, string>::iterator it;
 661                 bool error = false;
 662         map<string, int> thisCount;
 663         if (countfile != "") { thisCount = cparser->getCountTable(group);  }
 664
 665                 for (int i = 0; i < thisSeqs.size(); i++) {
 666
 667                         if (m->control_pressed) { return 0; }
 668
 669                         if (namefile != "") {
 670                                 it = thisName.find(thisSeqs[i].getName());
 671
 672                                 //should never be true since parser checks for this
 673                                 if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
 674                                 else{
 675                                         //get number of reps
 676                                         int numReps = 1;
 677                                         for(int j=0;j<(it->second).length();j++){
 678                                                 if((it->second)[j] == ','){     numReps++;      }
 679                                         }
 680
 681                                         seqPNode tempNode(numReps, thisSeqs[i], it->second);
 682                                         alignSeqs.push_back(tempNode);
 683                     lengths.insert(thisSeqs[i].getAligned().length());
 684                                 }
 685                         }else { //no names file, you are identical to yourself
 686                 int numRep = 1;
 687                 if (countfile != "") {
 688                     map<string, int>::iterator it2 = thisCount.find(thisSeqs[i].getName());
 689
 690                     //should never be true since parser checks for this
 691                     if (it2 == thisCount.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); error = true; }
 692                     else { numRep = it2->second;  }
 693                 }
 694                                 seqPNode tempNode(numRep, thisSeqs[i], thisSeqs[i].getName());
 695                                 alignSeqs.push_back(tempNode);
 696                                 lengths.insert(thisSeqs[i].getAligned().length());
 697                         }
 698                 }
 699
 700         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(); }
 701         else if (lengths.size() == 1) { length = *(lengths.begin()); }
 702
 703                 //sanity check
 704                 if (error) { m->control_pressed = true; }
 705
 706                 thisSeqs.clear();
 707
 708                 return alignSeqs.size();
 709         }
 710
 711         catch(exception& e) {
 712                 m->errorOut(e, "PreClusterCommand", "loadSeqs");
 713                 exit(1);
 714         }
 715 }
 716
 717 /**************************************************************************************************/
 718
 719 int PreClusterCommand::calcMisMatches(string seq1, string seq2){
 720         try {
 721                 int numBad = 0;
 722
 723                 for (int i = 0; i < seq1.length(); i++) {
 724                         //do they match
 725                         if (seq1[i] != seq2[i]) { numBad++; }
 726                         if (numBad > diffs) { return length;  } //to far to cluster
 727                 }
 728
 729                 return numBad;
 730         }
 731         catch(exception& e) {
 732                 m->errorOut(e, "PreClusterCommand", "calcMisMatches");
 733                 exit(1);
 734         }
 735 }
 736 /**************************************************************************************************/
 737
 738 int PreClusterCommand::mergeGroupCounts(string newcount, string newname, string newfasta){
 739         try {
 740                 ifstream inNames;
 741         m->openInputFile(newname, inNames);
 742
 743         string group, first, second;
 744         set<string> uniqueNames;
 745         while (!inNames.eof()) {
 746             if (m->control_pressed) { break; }
 747             inNames >> group; m->gobble(inNames);
 748             inNames >> first; m->gobble(inNames);
 749             inNames >> second; m->gobble(inNames);
 750
 751             vector<string> names;
 752             m->splitAtComma(second, names);
 753
 754             uniqueNames.insert(first);
 755
 756             int total = ct.getGroupCount(first, group);
 757             for (int i = 1; i < names.size(); i++) {
 758                 total += ct.getGroupCount(names[i], group);
 759                 ct.setAbund(names[i], group, 0);
 760             }
 761             ct.setAbund(first, group, total);
 762         }
 763         inNames.close();
 764
 765         vector<string> namesOfSeqs = ct.getNamesOfSeqs();
 766         for (int i = 0; i < namesOfSeqs.size(); i++) {
 767             if (ct.getNumSeqs(namesOfSeqs[i]) == 0) {
 768                 ct.remove(namesOfSeqs[i]);
 769             }
 770         }
 771
 772         ct.printTable(newcount);
 773         m->mothurRemove(newname);
 774
 775         if (bygroup) { //if by group, must remove the duplicate seqs that are named the same
 776             ifstream in;
 777             m->openInputFile(newfasta, in);
 778
 779             ofstream out;
 780             m->openOutputFile(newfasta+"temp", out);
 781
 782             int count = 0;
 783             set<string> already;
 784             while(!in.eof()) {
 785                 if (m->control_pressed) { break; }
 786
 787                 Sequence seq(in); m->gobble(in);
 788
 789                 if (seq.getName() != "") {
 790                     count++;
 791                     if (already.count(seq.getName()) == 0) {
 792                         seq.printSequence(out);
 793                         already.insert(seq.getName());
 794                     }
 795                 }
 796             }
 797             in.close();
 798             out.close();
 799             m->mothurRemove(newfasta);
 800             m->renameFile(newfasta+"temp", newfasta);
 801         }
 802                         return 0;
 803
 804         }
 805         catch(exception& e) {
 806                 m->errorOut(e, "PreClusterCommand", "mergeGroupCounts");
 807                 exit(1);
 808         }
 809 }
 810
 811 /**************************************************************************************************/
 812
 813 void PreClusterCommand::printData(string newfasta, string newname, string group){
 814         try {
 815                 ofstream outFasta;
 816                 ofstream outNames;
 817
 818                 if (bygroup) {
 819                         m->openOutputFileAppend(newfasta, outFasta);
 820                         m->openOutputFileAppend(newname, outNames);
 821                 }else {
 822                         m->openOutputFile(newfasta, outFasta);
 823                         m->openOutputFile(newname, outNames);
 824                 }
 825
 826         if ((countfile != "") && (group == ""))  { outNames << "Representative_Sequence\ttotal\n";  }
 827                 for (int i = 0; i < alignSeqs.size(); i++) {
 828                         if (alignSeqs[i].numIdentical != 0) {
 829                                 alignSeqs[i].seq.printSequence(outFasta);
 830                                 if (countfile != "") {
 831                     if (group != "") {  outNames << group << '\t' << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; }
 832                     else {  outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].numIdentical << endl;  }
 833                 }else {  outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;  }
 834                         }
 835                 }
 836
 837                 outFasta.close();
 838                 outNames.close();
 839
 840         }
 841         catch(exception& e) {
 842                 m->errorOut(e, "PreClusterCommand", "printData");
 843                 exit(1);
 844         }
 845 }
 846 /**************************************************************************************************/
 847
 848 void PreClusterCommand::readNameFile(){
 849         try {
 850                 ifstream in;
 851                 m->openInputFile(namefile, in);
 852                 string firstCol, secondCol;
 853
 854                 while (!in.eof()) {
 855                         in >> firstCol >> secondCol; m->gobble(in);
 856                         names[firstCol] = secondCol;
 857                         int size = 1;
 858
 859                         for(int i=0;i<secondCol.size();i++){
 860                                 if(secondCol[i] == ','){        size++; }
 861                         }
 862                         sizes[firstCol] = size;
 863                 }
 864                 in.close();
 865         }
 866         catch(exception& e) {
 867                 m->errorOut(e, "PreClusterCommand", "readNameFile");
 868                 exit(1);
 869         }
 870 }
 871
 872 /**************************************************************************************************/
 873
 874