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                         if (m->control_pressed) { return 0; }
 217
 218                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 219
 220                         if (outputDir == "") {  outputDir += hasPath(candidateFileNames[s]); }
 221                         string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
 222                         string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
 223                         string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
 224                         bool hasAccnos = true;
 225
 226                         int numFastaSeqs = 0;
 227                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 228                         int start = time(NULL);
 229
 230 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 231                         if(processors == 1){
 232                                 ifstream inFASTA;
 233                                 openInputFile(candidateFileNames[s], inFASTA);
 234                                 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 235                                 inFASTA.close();
 236
 237                                 lines.push_back(new linePair(0, numFastaSeqs));
 238
 239                                 driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 240
 241                                 if (m->control_pressed) {
 242                                         remove(accnosFileName.c_str());
 243                                         remove(alignFileName.c_str());
 244                                         remove(reportFileName.c_str());
 245                                         return 0;
 246                                 }
 247
 248                                 //delete accnos file if its blank else report to user
 249                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 250                                 else {
 251                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 252                                         if (!flip) {
 253                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 254                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 255                                         m->mothurOutEndLine();
 256                                 }
 257                         }
 258                         else{
 259                                 vector<int> positions;
 260                                 processIDS.resize(0);
 261
 262                                 ifstream inFASTA;
 263                                 openInputFile(candidateFileNames[s], inFASTA);
 264
 265                                 string input;
 266                                 while(!inFASTA.eof()){
 267                                         input = getline(inFASTA);
 268                                         if (input.length() != 0) {
 269                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 270                                         }
 271                                 }
 272                                 inFASTA.close();
 273
 274                                 numFastaSeqs = positions.size();
 275
 276                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 277
 278                                 for (int i = 0; i < processors; i++) {
 279                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 280                                         if(i == processors - 1){
 281                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 282                                         }
 283                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 284                                 }
 285
 286                                 createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 287
 288                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 289                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
 290
 291                                 //append alignment and report files
 292                                 for(int i=1;i<processors;i++){
 293                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 294                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 295
 296                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 297                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 298                                 }
 299
 300                                 vector<string> nonBlankAccnosFiles;
 301                                 //delete blank accnos files generated with multiple processes
 302                                 for(int i=0;i<processors;i++){
 303                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 304                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 305                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 306                                 }
 307
 308                                 //append accnos files
 309                                 if (nonBlankAccnosFiles.size() != 0) {
 310                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 311
 312                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 313                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
 314                                                 remove(nonBlankAccnosFiles[h].c_str());
 315                                         }
 316                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 317                                         if (!flip) {
 318                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 319                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 320                                         m->mothurOutEndLine();
 321                                 }else{ hasAccnos = false;  }
 322
 323                                 if (m->control_pressed) {
 324                                         remove(accnosFileName.c_str());
 325                                         remove(alignFileName.c_str());
 326                                         remove(reportFileName.c_str());
 327                                         return 0;
 328                                 }
 329                         }
 330 #else
 331                         ifstream inFASTA;
 332                         openInputFile(candidateFileNames[s], inFASTA);
 333                         numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 334                         inFASTA.close();
 335
 336                         lines.push_back(new linePair(0, numFastaSeqs));
 337
 338                         driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 339
 340                         if (m->control_pressed) {
 341                                 remove(accnosFileName.c_str());
 342                                 remove(alignFileName.c_str());
 343                                 remove(reportFileName.c_str());
 344                                 return 0;
 345                         }
 346
 347                         //delete accnos file if its blank else report to user
 348                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 349                         else {
 350                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 351                                 if (!flip) {
 352                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 353                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 354                                 m->mothurOutEndLine();
 355                         }
 356
 357 #endif
 358
 359                         outputNames.push_back(alignFileName);
 360                         outputNames.push_back(reportFileName);
 361                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);          }
 362
 363                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 364                         m->mothurOutEndLine();
 365                         m->mothurOutEndLine();
 366                 }
 367
 368
 369                 m->mothurOutEndLine();
 370                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 371                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 372                 m->mothurOutEndLine();
 373
 374                 return 0;
 375         }
 376         catch(exception& e) {
 377                 m->errorOut(e, "AlignCommand", "execute");
 378                 exit(1);
 379         }
 380 }
 381
 382 //**********************************************************************************************************************
 383
 384 int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
 385         try {
 386                 ofstream alignmentFile;
 387                 openOutputFile(alignFName, alignmentFile);
 388
 389                 ofstream accnosFile;
 390                 openOutputFile(accnosFName, accnosFile);
 391
 392                 NastReport report(reportFName);
 393
 394                 ifstream inFASTA;
 395                 openInputFile(filename, inFASTA);
 396
 397                 inFASTA.seekg(line->start);
 398
 399                 for(int i=0;i<line->numSeqs;i++){
 400
 401                         if (m->control_pressed) {  return 0; }
 402
 403                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 404                         int origNumBases = candidateSeq->getNumBases();
 405                         string originalUnaligned = candidateSeq->getUnaligned();
 406                         int numBasesNeeded = origNumBases * threshold;
 407
 408                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 409                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 410                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 411                                 }
 412
 413                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 414                                 Sequence* templateSeq = &temp;
 415
 416                                 float searchScore = templateDB->getSearchScore();
 417
 418                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 419                                 Sequence* copy;
 420
 421                                 Nast* nast2;
 422                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 423                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 424                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 425                                                                                                 //so this bool tells you if you need to delete it
 426
 427                                 //if there is a possibility that this sequence should be reversed
 428                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 429
 430                                         string wasBetter = "";
 431                                         //if the user wants you to try the reverse
 432                                         if (flip) {
 433                                                 //get reverse compliment
 434                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 435                                                 copy->reverseComplement();
 436
 437                                                 //rerun alignment
 438                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 439                                                 Sequence* templateSeq2 = &temp2;
 440
 441                                                 searchScore = templateDB->getSearchScore();
 442
 443                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 444
 445                                                 //check if any better
 446                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 447                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 448                                                         templateSeq = templateSeq2;
 449                                                         delete nast;
 450                                                         nast = nast2;
 451                                                         needToDeleteCopy = true;
 452                                                 }else{
 453                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 454                                                         delete nast2;
 455                                                         delete copy;
 456                                                 }
 457                                         }
 458
 459                                         //create accnos file with names
 460                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 461                                 }
 462
 463                                 report.setCandidate(candidateSeq);
 464                                 report.setTemplate(templateSeq);
 465                                 report.setSearchParameters(search, searchScore);
 466                                 report.setAlignmentParameters(align, alignment);
 467                                 report.setNastParameters(*nast);
 468
 469                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 470
 471                                 report.print();
 472                                 delete nast;
 473                                 if (needToDeleteCopy) {   delete copy;   }
 474                         }
 475                         delete candidateSeq;
 476
 477                         //report progress
 478                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 479                 }
 480                 //report progress
 481                 if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();           }
 482
 483                 alignmentFile.close();
 484                 inFASTA.close();
 485                 accnosFile.close();
 486
 487                 return 1;
 488         }
 489         catch(exception& e) {
 490                 m->errorOut(e, "AlignCommand", "driver");
 491                 exit(1);
 492         }
 493 }
 494
 495 /**************************************************************************************************/
 496
 497 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 498         try {
 499 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 500                 int process = 0;
 501                 int exitCommand = 1;
 502                 //              processIDS.resize(0);
 503
 504                 //loop through and create all the processes you want
 505                 while (process != processors) {
 506                         int pid = fork();
 507
 508                         if (pid > 0) {
 509                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 510                                 process++;
 511                         }else if (pid == 0){
 512                                 exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 513                                 exit(0);
 514                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 515                 }
 516
 517                 //force parent to wait until all the processes are done
 518                 for (int i=0;i<processors;i++) {
 519                         int temp = processIDS[i];
 520                         wait(&temp);
 521                 }
 522
 523                 return exitCommand;
 524 #endif
 525         }
 526         catch(exception& e) {
 527                 m->errorOut(e, "AlignCommand", "createProcesses");
 528                 exit(1);
 529         }
 530 }
 531
 532 /**************************************************************************************************/
 533
 534 void AlignCommand::appendAlignFiles(string temp, string filename) {
 535         try{
 536
 537                 ofstream output;
 538                 ifstream input;
 539                 openOutputFileAppend(filename, output);
 540                 openInputFile(temp, input);
 541
 542                 while(char c = input.get()){
 543                         if(input.eof())         {       break;                  }
 544                         else                            {       output << c;    }
 545                 }
 546
 547                 input.close();
 548                 output.close();
 549         }
 550         catch(exception& e) {
 551                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 552                 exit(1);
 553         }
 554 }
 555 //**********************************************************************************************************************
 556
 557 void AlignCommand::appendReportFiles(string temp, string filename) {
 558         try{
 559
 560                 ofstream output;
 561                 ifstream input;
 562                 openOutputFileAppend(filename, output);
 563                 openInputFile(temp, input);
 564
 565                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 566
 567                 while(char c = input.get()){
 568                         if(input.eof())         {       break;                  }
 569                         else                            {       output << c;    }
 570                 }
 571
 572                 input.close();
 573                 output.close();
 574         }
 575         catch(exception& e) {
 576                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 577                 exit(1);
 578         }
 579 }
 580
 581 //**********************************************************************************************************************