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 vector<string> AlignCommand::getValidParameters(){
  31         try {
  32                 string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
  33                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "AlignCommand", "getValidParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 vector<string> AlignCommand::getRequiredParameters(){
  43         try {
  44                 string AlignArray[] =  {"template","candidate"};
  45                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  46                 return myArray;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "AlignCommand", "getRequiredParameters");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 vector<string> AlignCommand::getRequiredFiles(){
  55         try {
  56                 vector<string> myArray;
  57                 return myArray;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "AlignCommand", "getRequiredFiles");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 AlignCommand::AlignCommand(){
  66         try {
  67                 //initialize outputTypes
  68                 vector<string> tempOutNames;
  69                 outputTypes["fasta"] = tempOutNames;
  70                 outputTypes["alignreport"] = tempOutNames;
  71                 outputTypes["accnos"] = tempOutNames;
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "AlignCommand", "AlignCommand");
  75                 exit(1);
  76         }
  77 }
  78 //**********************************************************************************************************************
  79 AlignCommand::AlignCommand(string option)  {
  80         try {
  81                 abort = false;
  82
  83                 //allow user to run help
  84                 if(option == "help") { help(); abort = true; }
  85
  86                 else {
  87
  88                         //valid paramters for this command
  89                         string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
  90                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  91
  92                         OptionParser parser(option);
  93                         map<string, string> parameters = parser.getParameters();
  94
  95                         ValidParameters validParameter("align.seqs");
  96                         map<string, string>::iterator it;
  97
  98                         //check to make sure all parameters are valid for command
  99                         for (it = parameters.begin(); it != parameters.end(); it++) {
 100                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 101                         }
 102
 103                         //initialize outputTypes
 104                         vector<string> tempOutNames;
 105                         outputTypes["fasta"] = tempOutNames;
 106                         outputTypes["alignreport"] = tempOutNames;
 107                         outputTypes["accnos"] = tempOutNames;
 108
 109                         //if the user changes the output directory command factory will send this info to us in the output parameter
 110                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 111
 112
 113                         //if the user changes the input directory command factory will send this info to us in the output parameter
 114                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 115
 116                         if (inputDir == "not found"){   inputDir = "";          }
 117                         else {
 118                                 string path;
 119
 120                                 it = parameters.find("template");
 121
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
 127                                 }
 128                         }
 129
 130                         //check for required parameters
 131                         templateFileName = validParameter.validFile(parameters, "template", true);
 132
 133                         if (templateFileName == "not found") {
 134                                 m->mothurOut("template is a required parameter for the align.seqs command.");
 135                                 m->mothurOutEndLine();
 136                                 abort = true;
 137                         }else if (templateFileName == "not open") { abort = true; }
 138
 139                         candidateFileName = validParameter.validFile(parameters, "candidate", false);
 140                         if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true;  }
 141                         else {
 142                                 m->splitAtDash(candidateFileName, candidateFileNames);
 143
 144                                 //go through files and make sure they are good, if not, then disregard them
 145                                 for (int i = 0; i < candidateFileNames.size(); i++) {
 146                                         //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
 147
 148                                         if (inputDir != "") {
 149                                                 string path = m->hasPath(candidateFileNames[i]);
 150                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 151                                                 if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
 152                                         }
 153
 154                                         int ableToOpen;
 155                                         ifstream in;
 156                                         ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
 157                                         in.close();
 158
 159                                         //if you can't open it, try default location
 160                                         if (ableToOpen == 1) {
 161                                                 if (m->getDefaultPath() != "") { //default path is set
 162                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
 163                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 164                                                         ifstream in2;
 165                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 166                                                         in2.close();
 167                                                         candidateFileNames[i] = tryPath;
 168                                                 }
 169                                         }
 170
 171                                         //if you can't open it, try default location
 172                                         if (ableToOpen == 1) {
 173                                                 if (m->getOutputDir() != "") { //default path is set
 174                                                         string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
 175                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 176                                                         ifstream in2;
 177                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 178                                                         in2.close();
 179                                                         candidateFileNames[i] = tryPath;
 180                                                 }
 181                                         }
 182
 183
 184
 185                                         if (ableToOpen == 1) {
 186                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 187                                                 //erase from file list
 188                                                 candidateFileNames.erase(candidateFileNames.begin()+i);
 189                                                 i--;
 190                                         }
 191
 192                                 }
 193
 194                                 //make sure there is at least one valid file left
 195                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 196                         }
 197
 198                         //check for optional parameter and set defaults
 199                         // ...at some point should added some additional type checking...
 200                         string temp;
 201                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 202                         convert(temp, kmerSize);
 203
 204                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 205                         convert(temp, match);
 206
 207                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 208                         convert(temp, misMatch);
 209
 210                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 211                         convert(temp, gapOpen);
 212
 213                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 214                         convert(temp, gapExtend);
 215
 216                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 217                         convert(temp, processors);
 218
 219                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 220                         flip = m->isTrue(temp);
 221
 222                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 223                         convert(temp, threshold);
 224
 225                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 226
 227                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 228                 }
 229
 230         }
 231         catch(exception& e) {
 232                 m->errorOut(e, "AlignCommand", "AlignCommand");
 233                 exit(1);
 234         }
 235 }
 236 //**********************************************************************************************************************
 237
 238 AlignCommand::~AlignCommand(){
 239
 240         if (abort == false) {
 241                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 242                 delete templateDB;
 243                 delete alignment;
 244         }
 245 }
 246
 247 //**********************************************************************************************************************
 248
 249 void AlignCommand::help(){
 250         try {
 251                 m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
 252                 m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen, gapextend and processors.\n");
 253                 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");
 254                 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");
 255                 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");
 256                 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 257                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 258                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 259                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 260                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 261                 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");
 262                 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");
 263                 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");
 264                 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");
 265                 m->mothurOut("The align.seqs command should be in the following format: \n");
 266                 m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
 267                 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");
 268                 m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
 269         }
 270         catch(exception& e) {
 271                 m->errorOut(e, "AlignCommand", "help");
 272                 exit(1);
 273         }
 274 }
 275
 276
 277 //**********************************************************************************************************************
 278
 279 int AlignCommand::execute(){
 280         try {
 281                 if (abort == true) {    return 0;       }
 282
 283                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 284                 int longestBase = templateDB->getLongestBase();
 285
 286                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 287                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 288                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 289                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 290                 else {
 291                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 292                         m->mothurOutEndLine();
 293                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 294                 }
 295
 296                 for (int s = 0; s < candidateFileNames.size(); s++) {
 297                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 298
 299                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 300
 301                         if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
 302                         string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
 303                         string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
 304                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
 305                         bool hasAccnos = true;
 306
 307                         int numFastaSeqs = 0;
 308                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 309                         int start = time(NULL);
 310
 311 #ifdef USE_MPI
 312                                 int pid, end, numSeqsPerProcessor;
 313                                 int tag = 2001;
 314                                 vector<unsigned long int> MPIPos;
 315                                 MPIWroteAccnos = false;
 316
 317                                 MPI_Status status;
 318                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 319                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 320
 321                                 MPI_File inMPI;
 322                                 MPI_File outMPIAlign;
 323                                 MPI_File outMPIReport;
 324                                 MPI_File outMPIAccnos;
 325
 326                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 327                                 int inMode=MPI_MODE_RDONLY;
 328
 329                                 char outAlignFilename[1024];
 330                                 strcpy(outAlignFilename, alignFileName.c_str());
 331
 332                                 char outReportFilename[1024];
 333                                 strcpy(outReportFilename, reportFileName.c_str());
 334
 335                                 char outAccnosFilename[1024];
 336                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 337
 338                                 char inFileName[1024];
 339                                 strcpy(inFileName, candidateFileNames[s].c_str());
 340
 341                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 342                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 343                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 344                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 345
 346                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 347
 348                                 if (pid == 0) { //you are the root process
 349
 350                                         MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 351
 352                                         //send file positions to all processes
 353                                         for(int i = 1; i < processors; i++) {
 354                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 355                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 356                                         }
 357
 358                                         //figure out how many sequences you have to align
 359                                         numSeqsPerProcessor = numFastaSeqs / processors;
 360                                         int startIndex =  pid * numSeqsPerProcessor;
 361                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 362
 363                                         //align your part
 364                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 365
 366                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 367
 368                                         for (int i = 1; i < processors; i++) {
 369                                                 bool tempResult;
 370                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 371                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 372                                         }
 373                                 }else{ //you are a child process
 374                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 375                                         MPIPos.resize(numFastaSeqs+1);
 376                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 377
 378
 379                                         //figure out how many sequences you have to align
 380                                         numSeqsPerProcessor = numFastaSeqs / processors;
 381                                         int startIndex =  pid * numSeqsPerProcessor;
 382                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 383
 384
 385                                         //align your part
 386                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 387
 388                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 389
 390                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 391                                 }
 392
 393                                 //close files
 394                                 MPI_File_close(&inMPI);
 395                                 MPI_File_close(&outMPIAlign);
 396                                 MPI_File_close(&outMPIReport);
 397                                 MPI_File_close(&outMPIAccnos);
 398
 399                                 //delete accnos file if blank
 400                                 if (pid == 0) {
 401                                         //delete accnos file if its blank else report to user
 402                                         if (MPIWroteAccnos) {
 403                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 404                                                 if (!flip) {
 405                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 406                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 407                                                 m->mothurOutEndLine();
 408                                         }else {
 409                                                 //MPI_Info info;
 410                                                 //MPI_File_delete(outAccnosFilename, info);
 411                                                 hasAccnos = false;
 412                                                 remove(accnosFileName.c_str());
 413                                         }
 414                                 }
 415
 416 #else
 417
 418                 vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
 419                 for (int i = 0; i < (positions.size()-1); i++) {
 420                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 421                 }
 422         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 423                         if(processors == 1){
 424                                 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 425
 426                                 if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
 427
 428                                 //delete accnos file if its blank else report to user
 429                                 if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 430                                 else {
 431                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 432                                         if (!flip) {
 433                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 434                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 435                                         m->mothurOutEndLine();
 436                                 }
 437                         }else{
 438                                 processIDS.resize(0);
 439
 440                                 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 441
 442                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 443                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
 444
 445                                 //append alignment and report files
 446                                 for(int i=1;i<processors;i++){
 447                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 448                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 449
 450                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 451                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 452                                 }
 453
 454                                 vector<string> nonBlankAccnosFiles;
 455                                 //delete blank accnos files generated with multiple processes
 456                                 for(int i=0;i<processors;i++){
 457                                         if (!(m->isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 458                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 459                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 460                                 }
 461
 462                                 //append accnos files
 463                                 if (nonBlankAccnosFiles.size() != 0) {
 464                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 465
 466                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 467                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
 468                                                 remove(nonBlankAccnosFiles[h].c_str());
 469                                         }
 470                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 471                                         if (!flip) {
 472                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 473                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 474                                         m->mothurOutEndLine();
 475                                 }else{ hasAccnos = false;  }
 476
 477                                 if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
 478                         }
 479         #else
 480                         numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 481
 482                         if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear();  return 0; }
 483
 484                         //delete accnos file if its blank else report to user
 485                         if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 486                         else {
 487                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 488                                 if (!flip) {
 489                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 490                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 491                                 m->mothurOutEndLine();
 492                         }
 493
 494         #endif
 495
 496 #endif
 497
 498
 499                 #ifdef USE_MPI
 500                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 501
 502                         if (pid == 0) { //only one process should output to screen
 503                 #endif
 504
 505                         outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
 506                         outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
 507                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);  }
 508
 509                 #ifdef USE_MPI
 510                         }
 511                 #endif
 512
 513                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 514                         m->mothurOutEndLine();
 515                         m->mothurOutEndLine();
 516                 }
 517
 518
 519                 m->mothurOutEndLine();
 520                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 521                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 522                 m->mothurOutEndLine();
 523
 524                 return 0;
 525         }
 526         catch(exception& e) {
 527                 m->errorOut(e, "AlignCommand", "execute");
 528                 exit(1);
 529         }
 530 }
 531
 532 //**********************************************************************************************************************
 533
 534 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
 535         try {
 536                 ofstream alignmentFile;
 537                 m->openOutputFile(alignFName, alignmentFile);
 538
 539                 ofstream accnosFile;
 540                 m->openOutputFile(accnosFName, accnosFile);
 541
 542                 NastReport report(reportFName);
 543
 544                 ifstream inFASTA;
 545                 m->openInputFile(filename, inFASTA);
 546
 547                 inFASTA.seekg(filePos->start);
 548
 549                 bool done = false;
 550                 int count = 0;
 551
 552                 while (!done) {
 553
 554                         if (m->control_pressed) {  return 0; }
 555
 556                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 557
 558                         int origNumBases = candidateSeq->getNumBases();
 559                         string originalUnaligned = candidateSeq->getUnaligned();
 560                         int numBasesNeeded = origNumBases * threshold;
 561
 562                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 563                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 564                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 565                                 }
 566
 567                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 568                                 Sequence* templateSeq = &temp;
 569
 570                                 float searchScore = templateDB->getSearchScore();
 571
 572                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 573
 574                                 Sequence* copy;
 575
 576                                 Nast* nast2;
 577                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 578                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 579                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 580                                                                                                 //so this bool tells you if you need to delete it
 581
 582                                 //if there is a possibility that this sequence should be reversed
 583                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 584
 585                                         string wasBetter =  "";
 586                                         //if the user wants you to try the reverse
 587                                         if (flip) {
 588
 589                                                 //get reverse compliment
 590                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 591                                                 copy->reverseComplement();
 592
 593                                                 //rerun alignment
 594                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 595                                                 Sequence* templateSeq2 = &temp2;
 596
 597                                                 searchScore = templateDB->getSearchScore();
 598
 599                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 600
 601                                                 //check if any better
 602                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 603                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 604                                                         templateSeq = templateSeq2;
 605                                                         delete nast;
 606                                                         nast = nast2;
 607                                                         needToDeleteCopy = true;
 608                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 609                                                 }else{
 610                                                         wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 611                                                         delete nast2;
 612                                                         delete copy;
 613                                                 }
 614                                         }
 615
 616                                         //create accnos file with names
 617                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 618                                 }
 619
 620                                 report.setCandidate(candidateSeq);
 621                                 report.setTemplate(templateSeq);
 622                                 report.setSearchParameters(search, searchScore);
 623                                 report.setAlignmentParameters(align, alignment);
 624                                 report.setNastParameters(*nast);
 625
 626                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 627
 628                                 report.print();
 629                                 delete nast;
 630                                 if (needToDeleteCopy) {   delete copy;   }
 631
 632                                 count++;
 633                         }
 634                         delete candidateSeq;
 635
 636                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 637                                 unsigned long int pos = inFASTA.tellg();
 638                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 639                         #else
 640                                 if (inFASTA.eof()) { break; }
 641                         #endif
 642
 643                         //report progress
 644                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 645
 646                 }
 647                 //report progress
 648                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 649
 650                 alignmentFile.close();
 651                 inFASTA.close();
 652                 accnosFile.close();
 653
 654                 return count;
 655         }
 656         catch(exception& e) {
 657                 m->errorOut(e, "AlignCommand", "driver");
 658                 exit(1);
 659         }
 660 }
 661 //**********************************************************************************************************************
 662 #ifdef USE_MPI
 663 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
 664         try {
 665                 string outputString = "";
 666                 MPI_Status statusReport;
 667                 MPI_Status statusAlign;
 668                 MPI_Status statusAccnos;
 669                 MPI_Status status;
 670                 int pid;
 671                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 672
 673                 NastReport report;
 674
 675                 if (pid == 0) {
 676                         outputString = report.getHeaders();
 677                         int length = outputString.length();
 678
 679                         char* buf = new char[length];
 680                         memcpy(buf, outputString.c_str(), length);
 681
 682                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 683
 684             delete buf;
 685                 }
 686
 687                 for(int i=0;i<num;i++){
 688
 689                         if (m->control_pressed) {  return 0; }
 690
 691                         //read next sequence
 692                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 693
 694                         char* buf4 = new char[length];
 695                         //memcpy(buf4, outputString.c_str(), length);
 696
 697                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 698
 699                         string tempBuf = buf4;
 700
 701                         delete buf4;
 702
 703                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 704
 705                         istringstream iss (tempBuf,istringstream::in);
 706
 707                         Sequence* candidateSeq = new Sequence(iss);
 708
 709                         int origNumBases = candidateSeq->getNumBases();
 710                         string originalUnaligned = candidateSeq->getUnaligned();
 711                         int numBasesNeeded = origNumBases * threshold;
 712
 713                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 714                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 715                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 716                                 }
 717
 718                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 719                                 Sequence* templateSeq = &temp;
 720
 721                                 float searchScore = templateDB->getSearchScore();
 722
 723                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 724                                 Sequence* copy;
 725
 726                                 Nast* nast2;
 727                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 728                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 729                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 730                                                                                                 //so this bool tells you if you need to delete it
 731
 732                                 //if there is a possibility that this sequence should be reversed
 733                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 734
 735                                         string wasBetter = "";
 736                                         //if the user wants you to try the reverse
 737                                         if (flip) {
 738                                                 //get reverse compliment
 739                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 740                                                 copy->reverseComplement();
 741
 742                                                 //rerun alignment
 743                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 744                                                 Sequence* templateSeq2 = &temp2;
 745
 746                                                 searchScore = templateDB->getSearchScore();
 747
 748                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 749
 750                                                 //check if any better
 751                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 752                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 753                                                         templateSeq = templateSeq2;
 754                                                         delete nast;
 755                                                         nast = nast2;
 756                                                         needToDeleteCopy = true;
 757                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 758                                                 }else{
 759                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 760                                                         delete nast2;
 761                                                         delete copy;
 762                                                 }
 763                                         }
 764
 765                                         //create accnos file with names
 766                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 767
 768                                         //send results to parent
 769                                         int length = outputString.length();
 770
 771                                         char* buf = new char[length];
 772                                         memcpy(buf, outputString.c_str(), length);
 773
 774                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 775                                         delete buf;
 776                                         MPIWroteAccnos = true;
 777                                 }
 778
 779                                 report.setCandidate(candidateSeq);
 780                                 report.setTemplate(templateSeq);
 781                                 report.setSearchParameters(search, searchScore);
 782                                 report.setAlignmentParameters(align, alignment);
 783                                 report.setNastParameters(*nast);
 784
 785                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 786
 787                                 //send results to parent
 788                                 int length = outputString.length();
 789                                 char* buf2 = new char[length];
 790                                 memcpy(buf2, outputString.c_str(), length);
 791
 792                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 793
 794                                 delete buf2;
 795
 796                                 outputString = report.getReport();
 797
 798                                 //send results to parent
 799                                 length = outputString.length();
 800                                 char* buf3 = new char[length];
 801                                 memcpy(buf3, outputString.c_str(), length);
 802
 803                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 804
 805                                 delete buf3;
 806                                 delete nast;
 807                                 if (needToDeleteCopy) {   delete copy;   }
 808                         }
 809                         delete candidateSeq;
 810
 811                         //report progress
 812                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 813                 }
 814                 //report progress
 815                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 816
 817                 return 1;
 818         }
 819         catch(exception& e) {
 820                 m->errorOut(e, "AlignCommand", "driverMPI");
 821                 exit(1);
 822         }
 823 }
 824 #endif
 825 /**************************************************************************************************/
 826
 827 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 828         try {
 829 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 830                 int process = 0;
 831                 int num = 0;
 832                 //              processIDS.resize(0);
 833
 834                 //loop through and create all the processes you want
 835                 while (process != processors) {
 836                         int pid = fork();
 837
 838                         if (pid > 0) {
 839                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 840                                 process++;
 841                         }else if (pid == 0){
 842                                 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 843
 844                                 //pass numSeqs to parent
 845                                 ofstream out;
 846                                 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
 847                                 m->openOutputFile(tempFile, out);
 848                                 out << num << endl;
 849                                 out.close();
 850
 851                                 exit(0);
 852                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 853                 }
 854
 855                 //force parent to wait until all the processes are done
 856                 for (int i=0;i<processors;i++) {
 857                         int temp = processIDS[i];
 858                         wait(&temp);
 859                 }
 860
 861                 for (int i = 0; i < processIDS.size(); i++) {
 862                         ifstream in;
 863                         string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
 864                         m->openInputFile(tempFile, in);
 865                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 866                         in.close(); remove(tempFile.c_str());
 867                 }
 868
 869                 return num;
 870 #endif
 871         }
 872         catch(exception& e) {
 873                 m->errorOut(e, "AlignCommand", "createProcesses");
 874                 exit(1);
 875         }
 876 }
 877 /**************************************************************************************************/
 878
 879 void AlignCommand::appendAlignFiles(string temp, string filename) {
 880         try{
 881
 882                 ofstream output;
 883                 ifstream input;
 884                 m->openOutputFileAppend(filename, output);
 885                 m->openInputFile(temp, input);
 886
 887                 while(char c = input.get()){
 888                         if(input.eof())         {       break;                  }
 889                         else                            {       output << c;    }
 890                 }
 891
 892                 input.close();
 893                 output.close();
 894         }
 895         catch(exception& e) {
 896                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 897                 exit(1);
 898         }
 899 }
 900 //**********************************************************************************************************************
 901
 902 void AlignCommand::appendReportFiles(string temp, string filename) {
 903         try{
 904
 905                 ofstream output;
 906                 ifstream input;
 907                 m->openOutputFileAppend(filename, output);
 908                 m->openInputFile(temp, input);
 909
 910                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 911
 912                 while(char c = input.get()){
 913                         if(input.eof())         {       break;                  }
 914                         else                            {       output << c;    }
 915                 }
 916
 917                 input.close();
 918                 output.close();
 919         }
 920         catch(exception& e) {
 921                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 922                 exit(1);
 923         }
 924 }
 925 //**********************************************************************************************************************