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("align.seqs");
  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
 102                                         #ifdef USE_MPI
 103                                                 int pid;
 104                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 105                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 106
 107                                                 if (pid == 0) {
 108                                         #endif
 109
 110                                         ableToOpen = openInputFile(candidateFileNames[i], in, "noerror");
 111
 112                                         //if you can't open it, try default location
 113                                         if (ableToOpen == 1) {
 114                                                 if (m->getDefaultPath() != "") { //default path is set
 115                                                         string tryPath = m->getDefaultPath() + getSimpleName(candidateFileNames[i]);
 116                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 117                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
 118                                                         candidateFileNames[i] = tryPath;
 119                                                 }
 120                                         }
 121                                         in.close();
 122                                         #ifdef USE_MPI
 123                                                         for (int j = 1; j < processors; j++) {
 124                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
 125                                                         }
 126                                                 }else{
 127                                                         MPI_Status status;
 128                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 129                                                 }
 130
 131                                         #endif
 132
 133                                         if (ableToOpen == 1) {
 134                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 135                                                 //erase from file list
 136                                                 candidateFileNames.erase(candidateFileNames.begin()+i);
 137                                                 i--;
 138                                         }
 139
 140                                 }
 141
 142                                 //make sure there is at least one valid file left
 143                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 144                         }
 145
 146                         //check for optional parameter and set defaults
 147                         // ...at some point should added some additional type checking...
 148                         string temp;
 149                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 150                         convert(temp, kmerSize);
 151
 152                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 153                         convert(temp, match);
 154
 155                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 156                         convert(temp, misMatch);
 157
 158                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 159                         convert(temp, gapOpen);
 160
 161                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 162                         convert(temp, gapExtend);
 163
 164                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 165                         convert(temp, processors);
 166
 167                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 168                         flip = isTrue(temp);
 169
 170                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 171                         convert(temp, threshold);
 172
 173                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 174
 175                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 176                 }
 177
 178         }
 179         catch(exception& e) {
 180                 m->errorOut(e, "AlignCommand", "AlignCommand");
 181                 exit(1);
 182         }
 183 }
 184
 185 //**********************************************************************************************************************
 186
 187 AlignCommand::~AlignCommand(){
 188
 189         if (abort == false) {
 190                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 191                 delete templateDB;
 192                 delete alignment;
 193         }
 194 }
 195
 196 //**********************************************************************************************************************
 197
 198 void AlignCommand::help(){
 199         try {
 200                 m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
 201                 m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
 202                 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");
 203                 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");
 204                 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");
 205                 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 206                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 207                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 208                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 209                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 210                 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");
 211                 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");
 212                 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");
 213                 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");
 214                 m->mothurOut("The align.seqs command should be in the following format: \n");
 215                 m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
 216                 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");
 217                 m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
 218         }
 219         catch(exception& e) {
 220                 m->errorOut(e, "AlignCommand", "help");
 221                 exit(1);
 222         }
 223 }
 224
 225
 226 //**********************************************************************************************************************
 227
 228 int AlignCommand::execute(){
 229         try {
 230                 if (abort == true) {    return 0;       }
 231
 232                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 233                 int longestBase = templateDB->getLongestBase();
 234
 235                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 236                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 237                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 238                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 239                 else {
 240                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 241                         m->mothurOutEndLine();
 242                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 243                 }
 244                 vector<string> outputNames;
 245
 246                 for (int s = 0; s < candidateFileNames.size(); s++) {
 247                         if (m->control_pressed) { return 0; }
 248
 249                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 250
 251                         if (outputDir == "") {  outputDir += hasPath(candidateFileNames[s]); }
 252                         string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
 253                         string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
 254                         string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
 255                         bool hasAccnos = true;
 256
 257                         int numFastaSeqs = 0;
 258                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 259                         int start = time(NULL);
 260
 261 #ifdef USE_MPI
 262                                 int pid, end, numSeqsPerProcessor;
 263                                 int tag = 2001;
 264                                 vector<unsigned long int> MPIPos;
 265                                 MPIWroteAccnos = false;
 266
 267                                 MPI_Status status;
 268                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 269                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 270
 271                                 MPI_File inMPI;
 272                                 MPI_File outMPIAlign;
 273                                 MPI_File outMPIReport;
 274                                 MPI_File outMPIAccnos;
 275
 276                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 277                                 int inMode=MPI_MODE_RDONLY;
 278
 279                                 char outAlignFilename[1024];
 280                                 strcpy(outAlignFilename, alignFileName.c_str());
 281
 282                                 char outReportFilename[1024];
 283                                 strcpy(outReportFilename, reportFileName.c_str());
 284
 285                                 char outAccnosFilename[1024];
 286                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 287
 288                                 char inFileName[1024];
 289                                 strcpy(inFileName, candidateFileNames[s].c_str());
 290
 291                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 292                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 293                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 294                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 295
 296                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 297
 298                                 if (pid == 0) { //you are the root process
 299
 300                                         MPIPos = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 301
 302                                         //send file positions to all processes
 303                                         for(int i = 1; i < processors; i++) {
 304                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 305                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 306                                         }
 307
 308                                         //figure out how many sequences you have to align
 309                                         numSeqsPerProcessor = numFastaSeqs / processors;
 310                                         int startIndex =  pid * numSeqsPerProcessor;
 311                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 312
 313
 314                                         //align your part
 315                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 316
 317                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 318
 319                                         for (int i = 1; i < processors; i++) {
 320                                                 bool tempResult;
 321                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 322                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 323                                         }
 324                                 }else{ //you are a child process
 325                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 326                                         MPIPos.resize(numFastaSeqs+1);
 327                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 328
 329
 330                                         //figure out how many sequences you have to align
 331                                         numSeqsPerProcessor = numFastaSeqs / processors;
 332                                         int startIndex =  pid * numSeqsPerProcessor;
 333                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 334
 335
 336                                         //align your part
 337                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 338
 339                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 340
 341                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 342                                 }
 343
 344                                 //close files
 345                                 MPI_File_close(&inMPI);
 346                                 MPI_File_close(&outMPIAlign);
 347                                 MPI_File_close(&outMPIReport);
 348                                 MPI_File_close(&outMPIAccnos);
 349
 350                                 //delete accnos file if blank
 351                                 if (pid == 0) {
 352                                         //delete accnos file if its blank else report to user
 353                                         if (MPIWroteAccnos) {
 354                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 355                                                 if (!flip) {
 356                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 357                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 358                                                 m->mothurOutEndLine();
 359                                         }else {
 360                                                 //MPI_Info info;
 361                                                 //MPI_File_delete(outAccnosFilename, info);
 362                                                 hasAccnos = false;
 363                                                 remove(accnosFileName.c_str());
 364                                         }
 365                                 }
 366
 367 #else
 368
 369         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 370                         if(processors == 1){
 371                                 ifstream inFASTA;
 372                                 openInputFile(candidateFileNames[s], inFASTA);
 373                                 getNumSeqs(inFASTA, numFastaSeqs);
 374                                 inFASTA.close();
 375
 376                                 lines.push_back(new linePair(0, numFastaSeqs));
 377
 378                                 driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 379
 380                                 if (m->control_pressed) {
 381                                         remove(accnosFileName.c_str());
 382                                         remove(alignFileName.c_str());
 383                                         remove(reportFileName.c_str());
 384                                         return 0;
 385                                 }
 386
 387                                 //delete accnos file if its blank else report to user
 388                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 389                                 else {
 390                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 391                                         if (!flip) {
 392                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 393                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 394                                         m->mothurOutEndLine();
 395                                 }
 396                         }
 397                         else{
 398                                 vector<unsigned long int> positions;
 399                                 processIDS.resize(0);
 400
 401                                 ifstream inFASTA;
 402                                 openInputFile(candidateFileNames[s], inFASTA);
 403
 404                                 string input;
 405                                 while(!inFASTA.eof()){
 406                                         input = getline(inFASTA);
 407                                         if (input.length() != 0) {
 408                                                 if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 409                                         }
 410                                 }
 411                                 inFASTA.close();
 412
 413                                 numFastaSeqs = positions.size();
 414
 415                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 416
 417                                 for (int i = 0; i < processors; i++) {
 418                                         unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
 419                                         if(i == processors - 1){
 420                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 421                                         }
 422                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 423                                 }
 424
 425                                 createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 426
 427                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 428                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
 429
 430                                 //append alignment and report files
 431                                 for(int i=1;i<processors;i++){
 432                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 433                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 434
 435                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 436                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 437                                 }
 438
 439                                 vector<string> nonBlankAccnosFiles;
 440                                 //delete blank accnos files generated with multiple processes
 441                                 for(int i=0;i<processors;i++){
 442                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 443                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 444                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 445                                 }
 446
 447                                 //append accnos files
 448                                 if (nonBlankAccnosFiles.size() != 0) {
 449                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 450
 451                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 452                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
 453                                                 remove(nonBlankAccnosFiles[h].c_str());
 454                                         }
 455                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 456                                         if (!flip) {
 457                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 458                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 459                                         m->mothurOutEndLine();
 460                                 }else{ hasAccnos = false;  }
 461
 462                                 if (m->control_pressed) {
 463                                         remove(accnosFileName.c_str());
 464                                         remove(alignFileName.c_str());
 465                                         remove(reportFileName.c_str());
 466                                         return 0;
 467                                 }
 468                         }
 469         #else
 470                         ifstream inFASTA;
 471                         openInputFile(candidateFileNames[s], inFASTA);
 472                         getNumSeqs(inFASTA, numFastaSeqs);
 473                         inFASTA.close();
 474
 475                         lines.push_back(new linePair(0, numFastaSeqs));
 476
 477                         driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 478
 479                         if (m->control_pressed) {
 480                                 remove(accnosFileName.c_str());
 481                                 remove(alignFileName.c_str());
 482                                 remove(reportFileName.c_str());
 483                                 return 0;
 484                         }
 485
 486                         //delete accnos file if its blank else report to user
 487                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 488                         else {
 489                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 490                                 if (!flip) {
 491                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 492                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 493                                 m->mothurOutEndLine();
 494                         }
 495
 496         #endif
 497
 498 #endif
 499
 500
 501                 #ifdef USE_MPI
 502                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 503
 504                         if (pid == 0) { //only one process should output to screen
 505                 #endif
 506
 507                         outputNames.push_back(alignFileName);
 508                         outputNames.push_back(reportFileName);
 509                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);          }
 510
 511                 #ifdef USE_MPI
 512                         }
 513                 #endif
 514
 515                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 516                         m->mothurOutEndLine();
 517                         m->mothurOutEndLine();
 518                 }
 519
 520
 521                 m->mothurOutEndLine();
 522                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 523                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 524                 m->mothurOutEndLine();
 525
 526                 return 0;
 527         }
 528         catch(exception& e) {
 529                 m->errorOut(e, "AlignCommand", "execute");
 530                 exit(1);
 531         }
 532 }
 533
 534 //**********************************************************************************************************************
 535
 536 int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
 537         try {
 538                 ofstream alignmentFile;
 539                 openOutputFile(alignFName, alignmentFile);
 540
 541                 ofstream accnosFile;
 542                 openOutputFile(accnosFName, accnosFile);
 543
 544                 NastReport report(reportFName);
 545
 546                 ifstream inFASTA;
 547                 openInputFile(filename, inFASTA);
 548
 549                 inFASTA.seekg(line->start);
 550
 551                 for(int i=0;i<line->numSeqs;i++){
 552
 553                         if (m->control_pressed) {  return 0; }
 554
 555                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 556
 557                         int origNumBases = candidateSeq->getNumBases();
 558                         string originalUnaligned = candidateSeq->getUnaligned();
 559                         int numBasesNeeded = origNumBases * threshold;
 560
 561                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 562                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 563                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 564                                 }
 565
 566                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 567                                 Sequence* templateSeq = &temp;
 568
 569                                 float searchScore = templateDB->getSearchScore();
 570
 571                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 572                                 Sequence* copy;
 573
 574                                 Nast* nast2;
 575                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 576                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 577                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 578                                                                                                 //so this bool tells you if you need to delete it
 579
 580                                 //if there is a possibility that this sequence should be reversed
 581                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 582
 583                                         string wasBetter = "";
 584                                         //if the user wants you to try the reverse
 585                                         if (flip) {
 586                                                 //get reverse compliment
 587                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 588                                                 copy->reverseComplement();
 589
 590                                                 //rerun alignment
 591                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 592                                                 Sequence* templateSeq2 = &temp2;
 593
 594                                                 searchScore = templateDB->getSearchScore();
 595
 596                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 597
 598                                                 //check if any better
 599                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 600                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 601                                                         templateSeq = templateSeq2;
 602                                                         delete nast;
 603                                                         nast = nast2;
 604                                                         needToDeleteCopy = true;
 605                                                 }else{
 606                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 607                                                         delete nast2;
 608                                                         delete copy;
 609                                                 }
 610                                         }
 611
 612                                         //create accnos file with names
 613                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 614                                 }
 615
 616                                 report.setCandidate(candidateSeq);
 617                                 report.setTemplate(templateSeq);
 618                                 report.setSearchParameters(search, searchScore);
 619                                 report.setAlignmentParameters(align, alignment);
 620                                 report.setNastParameters(*nast);
 621
 622                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 623
 624                                 report.print();
 625                                 delete nast;
 626                                 if (needToDeleteCopy) {   delete copy;   }
 627                         }
 628                         delete candidateSeq;
 629
 630                         //report progress
 631                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 632                 }
 633                 //report progress
 634                 if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();           }
 635
 636                 alignmentFile.close();
 637                 inFASTA.close();
 638                 accnosFile.close();
 639
 640                 return 1;
 641         }
 642         catch(exception& e) {
 643                 m->errorOut(e, "AlignCommand", "driver");
 644                 exit(1);
 645         }
 646 }
 647 //**********************************************************************************************************************
 648 #ifdef USE_MPI
 649 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
 650         try {
 651                 string outputString = "";
 652                 MPI_Status statusReport;
 653                 MPI_Status statusAlign;
 654                 MPI_Status statusAccnos;
 655                 MPI_Status status;
 656                 int pid;
 657                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 658
 659                 NastReport report;
 660
 661                 if (pid == 0) {
 662                         outputString = report.getHeaders();
 663                         int length = outputString.length();
 664
 665                         char* buf = new char[length];
 666                         memcpy(buf, outputString.c_str(), length);
 667
 668                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 669
 670             delete buf;
 671                 }
 672
 673                 for(int i=0;i<num;i++){
 674
 675                         if (m->control_pressed) {  return 0; }
 676
 677                         //read next sequence
 678                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 679
 680                         char* buf4 = new char[length];
 681                         memcpy(buf4, outputString.c_str(), length);
 682
 683                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 684
 685                         string tempBuf = buf4;
 686
 687                         delete buf4;
 688
 689                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 690                         istringstream iss (tempBuf,istringstream::in);
 691
 692                         Sequence* candidateSeq = new Sequence(iss);
 693                         int origNumBases = candidateSeq->getNumBases();
 694                         string originalUnaligned = candidateSeq->getUnaligned();
 695                         int numBasesNeeded = origNumBases * threshold;
 696
 697                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 698                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 699                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 700                                 }
 701
 702                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 703                                 Sequence* templateSeq = &temp;
 704
 705                                 float searchScore = templateDB->getSearchScore();
 706
 707                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 708                                 Sequence* copy;
 709
 710                                 Nast* nast2;
 711                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 712                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 713                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 714                                                                                                 //so this bool tells you if you need to delete it
 715
 716                                 //if there is a possibility that this sequence should be reversed
 717                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 718
 719                                         string wasBetter = "";
 720                                         //if the user wants you to try the reverse
 721                                         if (flip) {
 722                                                 //get reverse compliment
 723                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 724                                                 copy->reverseComplement();
 725
 726                                                 //rerun alignment
 727                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 728                                                 Sequence* templateSeq2 = &temp2;
 729
 730                                                 searchScore = templateDB->getSearchScore();
 731
 732                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 733
 734                                                 //check if any better
 735                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 736                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 737                                                         templateSeq = templateSeq2;
 738                                                         delete nast;
 739                                                         nast = nast2;
 740                                                         needToDeleteCopy = true;
 741                                                 }else{
 742                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 743                                                         delete nast2;
 744                                                         delete copy;
 745                                                 }
 746                                         }
 747
 748                                         //create accnos file with names
 749                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 750
 751                                         //send results to parent
 752                                         int length = outputString.length();
 753
 754                                         char* buf = new char[length];
 755                                         memcpy(buf, outputString.c_str(), length);
 756
 757                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 758                                         delete buf;
 759                                         MPIWroteAccnos = true;
 760                                 }
 761
 762                                 report.setCandidate(candidateSeq);
 763                                 report.setTemplate(templateSeq);
 764                                 report.setSearchParameters(search, searchScore);
 765                                 report.setAlignmentParameters(align, alignment);
 766                                 report.setNastParameters(*nast);
 767
 768                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 769
 770                                 //send results to parent
 771                                 int length = outputString.length();
 772                                 char* buf2 = new char[length];
 773                                 memcpy(buf2, outputString.c_str(), length);
 774
 775                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 776
 777                                 delete buf2;
 778
 779                                 outputString = report.getReport();
 780
 781                                 //send results to parent
 782                                 length = outputString.length();
 783                                 char* buf3 = new char[length];
 784                                 memcpy(buf3, outputString.c_str(), length);
 785
 786                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 787
 788                                 delete buf3;
 789                                 delete nast;
 790                                 if (needToDeleteCopy) {   delete copy;   }
 791                         }
 792                         delete candidateSeq;
 793
 794                         //report progress
 795                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 796                 }
 797                 //report progress
 798                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 799
 800                 return 1;
 801         }
 802         catch(exception& e) {
 803                 m->errorOut(e, "AlignCommand", "driverMPI");
 804                 exit(1);
 805         }
 806 }
 807 #endif
 808 /**************************************************************************************************/
 809
 810 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 811         try {
 812 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 813                 int process = 0;
 814                 int exitCommand = 1;
 815                 //              processIDS.resize(0);
 816
 817                 //loop through and create all the processes you want
 818                 while (process != processors) {
 819                         int pid = fork();
 820
 821                         if (pid > 0) {
 822                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 823                                 process++;
 824                         }else if (pid == 0){
 825                                 exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 826                                 exit(0);
 827                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 828                 }
 829
 830                 //force parent to wait until all the processes are done
 831                 for (int i=0;i<processors;i++) {
 832                         int temp = processIDS[i];
 833                         wait(&temp);
 834                 }
 835
 836                 return exitCommand;
 837 #endif
 838         }
 839         catch(exception& e) {
 840                 m->errorOut(e, "AlignCommand", "createProcesses");
 841                 exit(1);
 842         }
 843 }
 844
 845 /**************************************************************************************************/
 846
 847 void AlignCommand::appendAlignFiles(string temp, string filename) {
 848         try{
 849
 850                 ofstream output;
 851                 ifstream input;
 852                 openOutputFileAppend(filename, output);
 853                 openInputFile(temp, input);
 854
 855                 while(char c = input.get()){
 856                         if(input.eof())         {       break;                  }
 857                         else                            {       output << c;    }
 858                 }
 859
 860                 input.close();
 861                 output.close();
 862         }
 863         catch(exception& e) {
 864                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 865                 exit(1);
 866         }
 867 }
 868 //**********************************************************************************************************************
 869
 870 void AlignCommand::appendReportFiles(string temp, string filename) {
 871         try{
 872
 873                 ofstream output;
 874                 ifstream input;
 875                 openOutputFileAppend(filename, output);
 876                 openInputFile(temp, input);
 877
 878                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 879
 880                 while(char c = input.get()){
 881                         if(input.eof())         {       break;                  }
 882                         else                            {       output << c;    }
 883                 }
 884
 885                 input.close();
 886                 output.close();
 887         }
 888         catch(exception& e) {
 889                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 890                 exit(1);
 891         }
 892 }
 893 //**********************************************************************************************************************