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