aligncommand.cpp

   1 /*
   2  *  aligncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/15/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  *      This version of nast does everything I think that the greengenes nast server does and then some.  I have added the
   9  *      feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
  10  *      method.  This latter feature is perhaps most significant.  nastPlus enables a user to use either a Needleman-Wunsch
  11  *      (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm.  This is significant because it
  12  *      allows for a global alignment and not the local alignment provided by bLAst.  Furthermore, it has the potential to
  13  *      provide a better alignment because of the banding method employed by blast (I'm not sure about this).
  14  *
  15  */
  16
  17 #include "aligncommand.h"
  18 #include "sequence.hpp"
  19
  20 #include "gotohoverlap.hpp"
  21 #include "needlemanoverlap.hpp"
  22 #include "blastalign.hpp"
  23 #include "noalign.hpp"
  24
  25 #include "nast.hpp"
  26 #include "nastreport.hpp"
  27
  28
  29 //**********************************************************************************************************************
  30
  31 AlignCommand::AlignCommand(string option)  {
  32         try {
  33
  34                 abort = false;
  35
  36                 //allow user to run help
  37                 if(option == "help") { help(); abort = true; }
  38
  39                 else {
  40
  41                         //valid paramters for this command
  42                         string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
  43                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  44
  45                         OptionParser parser(option);
  46                         map<string, string> parameters = parser.getParameters();
  47
  48                         ValidParameters validParameter;
  49                         map<string, string>::iterator it;
  50
  51                         //check to make sure all parameters are valid for command
  52                         for (it = parameters.begin(); it != parameters.end(); it++) {
  53                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  54                         }
  55
  56                         //if the user changes the output directory command factory will send this info to us in the output parameter
  57                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  58
  59
  60                         //if the user changes the input directory command factory will send this info to us in the output parameter
  61                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  62
  63                         if (inputDir == "not found"){   inputDir = "";          }
  64                         else {
  65                                 string path;
  66
  67                                 it = parameters.find("template");
  68
  69                                 //user has given a template file
  70                                 if(it != parameters.end()){
  71                                         path = hasPath(it->second);
  72                                         //if the user has not given a path then, add inputdir. else leave path alone.
  73                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  74                                 }
  75                         }
  76
  77                         //check for required parameters
  78                         templateFileName = validParameter.validFile(parameters, "template", true);
  79
  80                         if (templateFileName == "not found") {
  81                                 m->mothurOut("template is a required parameter for the align.seqs command.");
  82                                 m->mothurOutEndLine();
  83                                 abort = true;
  84                         }else if (templateFileName == "not open") { abort = true; }
  85
  86                         candidateFileName = validParameter.validFile(parameters, "candidate", false);
  87                         if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true;  }
  88                         else {
  89                                 splitAtDash(candidateFileName, candidateFileNames);
  90
  91                                 //go through files and make sure they are good, if not, then disregard them
  92                                 for (int i = 0; i < candidateFileNames.size(); i++) {
  93                                         if (inputDir != "") {
  94                                                 string path = hasPath(candidateFileNames[i]);
  95                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  96                                                 if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
  97                                         }
  98
  99                                         int ableToOpen;
 100                                         ifstream in;
 101                                         ableToOpen = openInputFile(candidateFileNames[i], in);
 102                                         if (ableToOpen == 1) {
 103                                                 m->mothurOut(candidateFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
 104                                                 //erase from file list
 105                                                 candidateFileNames.erase(candidateFileNames.begin()+i);
 106                                                 i--;
 107                                         }
 108                                         in.close();
 109                                 }
 110
 111                                 //make sure there is at least one valid file left
 112                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 113                         }
 114
 115                         //check for optional parameter and set defaults
 116                         // ...at some point should added some additional type checking...
 117                         string temp;
 118                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 119                         convert(temp, kmerSize);
 120
 121                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 122                         convert(temp, match);
 123
 124                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 125                         convert(temp, misMatch);
 126
 127                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 128                         convert(temp, gapOpen);
 129
 130                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 131                         convert(temp, gapExtend);
 132
 133                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 134                         convert(temp, processors);
 135
 136                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 137                         flip = isTrue(temp);
 138
 139                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 140                         convert(temp, threshold);
 141
 142                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 143
 144                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 145                 }
 146
 147         }
 148         catch(exception& e) {
 149                 m->errorOut(e, "AlignCommand", "AlignCommand");
 150                 exit(1);
 151         }
 152 }
 153
 154 //**********************************************************************************************************************
 155
 156 AlignCommand::~AlignCommand(){
 157
 158         if (abort == false) {
 159                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 160                 delete templateDB;
 161                 delete alignment;
 162         }
 163 }
 164
 165 //**********************************************************************************************************************
 166
 167 void AlignCommand::help(){
 168         try {
 169                 m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
 170                 m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
 171                 m->mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
 172                 m->mothurOut("The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer.\n");
 173                 m->mothurOut("The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
 174                 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 175                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 176                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 177                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 178                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 179                 m->mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold.  The default is false.\n");
 180                 m->mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n");
 181                 m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
 182                 m->mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");
 183                 m->mothurOut("The align.seqs command should be in the following format: \n");
 184                 m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
 185                 m->mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
 186                 m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
 187         }
 188         catch(exception& e) {
 189                 m->errorOut(e, "AlignCommand", "help");
 190                 exit(1);
 191         }
 192 }
 193
 194
 195 //**********************************************************************************************************************
 196
 197 int AlignCommand::execute(){
 198         try {
 199                 if (abort == true) {    return 0;       }
 200
 201                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 202                 int longestBase = templateDB->getLongestBase();
 203
 204                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 205                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 206                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 207                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 208                 else {
 209                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 210                         m->mothurOutEndLine();
 211                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 212                 }
 213                 vector<string> outputNames;
 214
 215                 for (int s = 0; s < candidateFileNames.size(); s++) {
 216                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 217
 218                         if (outputDir == "") {  outputDir += hasPath(candidateFileNames[s]); }
 219                         string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
 220                         string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
 221                         string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
 222                         bool hasAccnos = true;
 223
 224                         int numFastaSeqs = 0;
 225                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 226                         int start = time(NULL);
 227
 228 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 229                         if(processors == 1){
 230                                 ifstream inFASTA;
 231                                 openInputFile(candidateFileNames[s], inFASTA);
 232                                 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 233                                 inFASTA.close();
 234
 235                                 lines.push_back(new linePair(0, numFastaSeqs));
 236
 237                                 int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 238                                 if (exitCommand == 0) {
 239                                         remove(accnosFileName.c_str());
 240                                         remove(alignFileName.c_str());
 241                                         remove(reportFileName.c_str());
 242                                         return 0;
 243                                 }
 244
 245                                 //delete accnos file if its blank else report to user
 246                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 247                                 else {
 248                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 249                                         if (!flip) {
 250                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 251                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 252                                         m->mothurOutEndLine();
 253                                 }
 254                         }
 255                         else{
 256                                 vector<int> positions;
 257                                 processIDS.resize(0);
 258
 259                                 ifstream inFASTA;
 260                                 openInputFile(candidateFileNames[s], inFASTA);
 261
 262                                 string input;
 263                                 while(!inFASTA.eof()){
 264                                         input = getline(inFASTA);
 265                                         if (input.length() != 0) {
 266                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 267                                         }
 268                                 }
 269                                 inFASTA.close();
 270
 271                                 numFastaSeqs = positions.size();
 272
 273                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 274
 275                                 for (int i = 0; i < processors; i++) {
 276                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 277                                         if(i == processors - 1){
 278                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 279                                         }
 280                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 281                                 }
 282
 283                                 int exitCommand = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 284
 285                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 286                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
 287
 288                                 //append alignment and report files
 289                                 for(int i=1;i<processors;i++){
 290                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 291                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 292
 293                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 294                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 295                                 }
 296
 297                                 vector<string> nonBlankAccnosFiles;
 298                                 //delete blank accnos files generated with multiple processes
 299                                 for(int i=0;i<processors;i++){
 300                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 301                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 302                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 303                                 }
 304
 305                                 //append accnos files
 306                                 if (nonBlankAccnosFiles.size() != 0) {
 307                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 308
 309                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 310                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
 311                                                 remove(nonBlankAccnosFiles[h].c_str());
 312                                         }
 313                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 314                                         if (!flip) {
 315                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 316                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 317                                         m->mothurOutEndLine();
 318                                 }else{ hasAccnos = false;  }
 319
 320                                 if (exitCommand == 0) {
 321                                         remove(accnosFileName.c_str());
 322                                         remove(alignFileName.c_str());
 323                                         remove(reportFileName.c_str());
 324                                         return 0;
 325                                 }
 326                         }
 327 #else
 328                         ifstream inFASTA;
 329                         openInputFile(candidateFileNames[s], inFASTA);
 330                         numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 331                         inFASTA.close();
 332
 333                         lines.push_back(new linePair(0, numFastaSeqs));
 334
 335                         int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 336                         if (exitCommand == 0) {
 337                                 remove(accnosFileName.c_str());
 338                                 remove(alignFileName.c_str());
 339                                 remove(reportFileName.c_str());
 340                                 return 0;
 341                         }
 342
 343                         //delete accnos file if its blank else report to user
 344                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 345                         else {
 346                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 347                                 if (!flip) {
 348                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 349                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 350                                 m->mothurOutEndLine();
 351                         }
 352
 353 #endif
 354
 355                         outputNames.push_back(alignFileName);
 356                         outputNames.push_back(reportFileName);
 357                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);          }
 358
 359                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 360                         m->mothurOutEndLine();
 361                         m->mothurOutEndLine();
 362                 }
 363
 364
 365                 m->mothurOutEndLine();
 366                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 367                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 368                 m->mothurOutEndLine();
 369
 370                 return 0;
 371         }
 372         catch(exception& e) {
 373                 m->errorOut(e, "AlignCommand", "execute");
 374                 exit(1);
 375         }
 376 }
 377
 378 //**********************************************************************************************************************
 379
 380 int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
 381         try {
 382                 ofstream alignmentFile;
 383                 openOutputFile(alignFName, alignmentFile);
 384
 385                 ofstream accnosFile;
 386                 openOutputFile(accnosFName, accnosFile);
 387
 388                 NastReport report(reportFName);
 389
 390                 ifstream inFASTA;
 391                 openInputFile(filename, inFASTA);
 392
 393                 inFASTA.seekg(line->start);
 394
 395                 for(int i=0;i<line->numSeqs;i++){
 396
 397                         if (m->control_pressed) {  return 0; }
 398
 399                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 400                         int origNumBases = candidateSeq->getNumBases();
 401                         string originalUnaligned = candidateSeq->getUnaligned();
 402                         int numBasesNeeded = origNumBases * threshold;
 403
 404                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 405                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 406                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 407                                 }
 408
 409                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 410                                 Sequence* templateSeq = &temp;
 411
 412                                 float searchScore = templateDB->getSearchScore();
 413
 414                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 415                                 Sequence* copy;
 416
 417                                 Nast* nast2;
 418                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 419                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 420                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 421                                                                                                 //so this bool tells you if you need to delete it
 422
 423                                 //if there is a possibility that this sequence should be reversed
 424                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 425
 426                                         string wasBetter = "";
 427                                         //if the user wants you to try the reverse
 428                                         if (flip) {
 429                                                 //get reverse compliment
 430                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 431                                                 copy->reverseComplement();
 432
 433                                                 //rerun alignment
 434                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 435                                                 Sequence* templateSeq2 = &temp2;
 436
 437                                                 searchScore = templateDB->getSearchScore();
 438
 439                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 440
 441                                                 //check if any better
 442                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 443                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 444                                                         templateSeq = templateSeq2;
 445                                                         delete nast;
 446                                                         nast = nast2;
 447                                                         needToDeleteCopy = true;
 448                                                 }else{
 449                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 450                                                         delete nast2;
 451                                                         delete copy;
 452                                                 }
 453                                         }
 454
 455                                         //create accnos file with names
 456                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 457                                 }
 458
 459                                 report.setCandidate(candidateSeq);
 460                                 report.setTemplate(templateSeq);
 461                                 report.setSearchParameters(search, searchScore);
 462                                 report.setAlignmentParameters(align, alignment);
 463                                 report.setNastParameters(*nast);
 464
 465                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 466
 467                                 report.print();
 468                                 delete nast;
 469                                 if (needToDeleteCopy) {   delete copy;   }
 470                         }
 471                         delete candidateSeq;
 472
 473                         //report progress
 474                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 475                 }
 476                 //report progress
 477                 if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();           }
 478
 479                 alignmentFile.close();
 480                 inFASTA.close();
 481                 accnosFile.close();
 482
 483                 return 1;
 484         }
 485         catch(exception& e) {
 486                 m->errorOut(e, "AlignCommand", "driver");
 487                 exit(1);
 488         }
 489 }
 490
 491 /**************************************************************************************************/
 492
 493 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 494         try {
 495 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 496                 int process = 0;
 497                 int exitCommand;
 498                 //              processIDS.resize(0);
 499
 500                 //loop through and create all the processes you want
 501                 while (process != processors) {
 502                         int pid = fork();
 503
 504                         if (pid > 0) {
 505                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 506                                 process++;
 507                         }else if (pid == 0){
 508                                 exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 509                                 exit(0);
 510                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 511                 }
 512
 513                 //force parent to wait until all the processes are done
 514                 for (int i=0;i<processors;i++) {
 515                         int temp = processIDS[i];
 516                         wait(&temp);
 517                 }
 518
 519                 return exitCommand;
 520 #endif
 521         }
 522         catch(exception& e) {
 523                 m->errorOut(e, "AlignCommand", "createProcesses");
 524                 exit(1);
 525         }
 526 }
 527
 528 /**************************************************************************************************/
 529
 530 void AlignCommand::appendAlignFiles(string temp, string filename) {
 531         try{
 532
 533                 ofstream output;
 534                 ifstream input;
 535                 openOutputFileAppend(filename, output);
 536                 openInputFile(temp, input);
 537
 538                 while(char c = input.get()){
 539                         if(input.eof())         {       break;                  }
 540                         else                            {       output << c;    }
 541                 }
 542
 543                 input.close();
 544                 output.close();
 545         }
 546         catch(exception& e) {
 547                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 548                 exit(1);
 549         }
 550 }
 551 //**********************************************************************************************************************
 552
 553 void AlignCommand::appendReportFiles(string temp, string filename) {
 554         try{
 555
 556                 ofstream output;
 557                 ifstream input;
 558                 openOutputFileAppend(filename, output);
 559                 openInputFile(temp, input);
 560
 561                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 562
 563                 while(char c = input.get()){
 564                         if(input.eof())         {       break;                  }
 565                         else                            {       output << c;    }
 566                 }
 567
 568                 input.close();
 569                 output.close();
 570         }
 571         catch(exception& e) {
 572                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 573                 exit(1);
 574         }
 575 }
 576
 577 //**********************************************************************************************************************