aligncommand.cpp

   1 /*
   2  *  aligncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/15/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  *      This version of nast does everything I think that the greengenes nast server does and then some.  I have added the
   9  *      feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
  10  *      method.  This latter feature is perhaps most significant.  nastPlus enables a user to use either a Needleman-Wunsch
  11  *      (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm.  This is significant because it
  12  *      allows for a global alignment and not the local alignment provided by bLAst.  Furthermore, it has the potential to
  13  *      provide a better alignment because of the banding method employed by blast (I'm not sure about this).
  14  *
  15  */
  16
  17 #include "aligncommand.h"
  18 #include "sequence.hpp"
  19
  20 #include "gotohoverlap.hpp"
  21 #include "needlemanoverlap.hpp"
  22 #include "blastalign.hpp"
  23 #include "noalign.hpp"
  24
  25 #include "nast.hpp"
  26 #include "nastreport.hpp"
  27
  28
  29 //**********************************************************************************************************************
  30
  31 AlignCommand::AlignCommand(string option)  {
  32         try {
  33
  34                 abort = false;
  35
  36                 //allow user to run help
  37                 if(option == "help") { help(); abort = true; }
  38
  39                 else {
  40
  41                         //valid paramters for this command
  42                         string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
  43                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  44
  45                         OptionParser parser(option);
  46                         map<string, string> parameters = parser.getParameters();
  47
  48                         ValidParameters validParameter;
  49                         map<string, string>::iterator it;
  50
  51                         //check to make sure all parameters are valid for command
  52                         for (it = parameters.begin(); it != parameters.end(); it++) {
  53                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  54                         }
  55
  56                         //if the user changes the output directory command factory will send this info to us in the output parameter
  57                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  58
  59
  60                         //if the user changes the input directory command factory will send this info to us in the output parameter
  61                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  62
  63                         if (inputDir == "not found"){   inputDir = "";          }
  64                         else {
  65                                 string path;
  66
  67                                 it = parameters.find("template");
  68
  69                                 //user has given a template file
  70                                 if(it != parameters.end()){
  71                                         path = hasPath(it->second);
  72                                         //if the user has not given a path then, add inputdir. else leave path alone.
  73                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  74                                 }
  75                         }
  76
  77                         //check for required parameters
  78                         templateFileName = validParameter.validFile(parameters, "template", true);
  79
  80                         if (templateFileName == "not found") {
  81                                 m->mothurOut("template is a required parameter for the align.seqs command.");
  82                                 m->mothurOutEndLine();
  83                                 abort = true;
  84                         }else if (templateFileName == "not open") { abort = true; }
  85
  86                         candidateFileName = validParameter.validFile(parameters, "candidate", false);
  87                         if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true;  }
  88                         else {
  89                                 splitAtDash(candidateFileName, candidateFileNames);
  90
  91                                 //go through files and make sure they are good, if not, then disregard them
  92                                 for (int i = 0; i < candidateFileNames.size(); i++) {
  93                                         if (inputDir != "") {
  94                                                 string path = hasPath(candidateFileNames[i]);
  95                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  96                                                 if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
  97                                         }
  98
  99                                         int ableToOpen;
 100                                         ifstream in;
 101
 102                                         #ifdef USE_MPI
 103                                                 int pid;
 104                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 105                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 106
 107                                                 if (pid == 0) {
 108                                         #endif
 109
 110                                         ableToOpen = openInputFile(candidateFileNames[i], in);
 111                                         in.close();
 112
 113                                         #ifdef USE_MPI
 114                                                         for (int j = 1; j < processors; j++) {
 115                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
 116                                                         }
 117                                                 }else{
 118                                                         MPI_Status status;
 119                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 120                                                 }
 121
 122                                         #endif
 123
 124                                         if (ableToOpen == 1) {
 125                                                 m->mothurOut(candidateFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
 126                                                 //erase from file list
 127                                                 candidateFileNames.erase(candidateFileNames.begin()+i);
 128                                                 i--;
 129                                         }
 130
 131                                 }
 132
 133                                 //make sure there is at least one valid file left
 134                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 135                         }
 136
 137                         //check for optional parameter and set defaults
 138                         // ...at some point should added some additional type checking...
 139                         string temp;
 140                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 141                         convert(temp, kmerSize);
 142
 143                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 144                         convert(temp, match);
 145
 146                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 147                         convert(temp, misMatch);
 148
 149                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 150                         convert(temp, gapOpen);
 151
 152                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 153                         convert(temp, gapExtend);
 154
 155                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 156                         convert(temp, processors);
 157
 158                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 159                         flip = isTrue(temp);
 160
 161                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 162                         convert(temp, threshold);
 163
 164                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 165
 166                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 167                 }
 168
 169         }
 170         catch(exception& e) {
 171                 m->errorOut(e, "AlignCommand", "AlignCommand");
 172                 exit(1);
 173         }
 174 }
 175
 176 //**********************************************************************************************************************
 177
 178 AlignCommand::~AlignCommand(){
 179
 180         if (abort == false) {
 181                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 182                 delete templateDB;
 183                 delete alignment;
 184         }
 185 }
 186
 187 //**********************************************************************************************************************
 188
 189 void AlignCommand::help(){
 190         try {
 191                 m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
 192                 m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
 193                 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");
 194                 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");
 195                 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");
 196                 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 197                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 198                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 199                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 200                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 201                 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");
 202                 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");
 203                 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");
 204                 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");
 205                 m->mothurOut("The align.seqs command should be in the following format: \n");
 206                 m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
 207                 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");
 208                 m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
 209         }
 210         catch(exception& e) {
 211                 m->errorOut(e, "AlignCommand", "help");
 212                 exit(1);
 213         }
 214 }
 215
 216
 217 //**********************************************************************************************************************
 218
 219 int AlignCommand::execute(){
 220         try {
 221                 if (abort == true) {    return 0;       }
 222
 223                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 224                 int longestBase = templateDB->getLongestBase();
 225
 226                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 227                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 228                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 229                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 230                 else {
 231                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 232                         m->mothurOutEndLine();
 233                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 234                 }
 235                 vector<string> outputNames;
 236
 237                 for (int s = 0; s < candidateFileNames.size(); s++) {
 238                         if (m->control_pressed) { return 0; }
 239
 240                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 241
 242                         if (outputDir == "") {  outputDir += hasPath(candidateFileNames[s]); }
 243                         string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
 244                         string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
 245                         string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
 246                         bool hasAccnos = true;
 247
 248                         int numFastaSeqs = 0;
 249                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 250                         int start = time(NULL);
 251
 252 #ifdef USE_MPI
 253                                 int pid, end, numSeqsPerProcessor;
 254                                 int tag = 2001;
 255                                 vector<long> MPIPos;
 256                                 MPIWroteAccnos = false;
 257
 258                                 MPI_Status status;
 259                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 260                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 261
 262                                 MPI_File inMPI;
 263                                 MPI_File outMPIAlign;
 264                                 MPI_File outMPIReport;
 265                                 MPI_File outMPIAccnos;
 266
 267                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 268                                 int inMode=MPI_MODE_RDONLY;
 269
 270                                 //char* outAlignFilename = new char[alignFileName.length()];
 271                                 //memcpy(outAlignFilename, alignFileName.c_str(), alignFileName.length());
 272
 273                                 char outAlignFilename[1024];
 274                                 strcpy(outAlignFilename, alignFileName.c_str());
 275
 276                                 //char* outReportFilename = new char[reportFileName.length()];
 277                                 //memcpy(outReportFilename, reportFileName.c_str(), reportFileName.length());
 278
 279                                 char outReportFilename[1024];
 280                                 strcpy(outReportFilename, reportFileName.c_str());
 281
 282                                 //char* outAccnosFilename = new char[accnosFileName.length()];
 283                                 //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
 284
 285                                 char outAccnosFilename[1024];
 286                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 287
 288                                 //char* inFileName = new char[candidateFileNames[s].length()];
 289                                 //memcpy(inFileName, candidateFileNames[s].c_str(), candidateFileNames[s].length());
 290
 291                                 char inFileName[1024];
 292                                 strcpy(inFileName, candidateFileNames[s].c_str());
 293
 294                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 295                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 296                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 297                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 298
 299                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 300
 301                                 if (pid == 0) { //you are the root process
 302
 303                                         MPIPos = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 304
 305                                         //send file positions to all processes
 306                                         for(int i = 1; i < processors; i++) {
 307                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 308                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 309                                         }
 310
 311                                         //figure out how many sequences you have to align
 312                                         numSeqsPerProcessor = numFastaSeqs / processors;
 313                                         int startIndex =  pid * numSeqsPerProcessor;
 314                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 315
 316
 317                                         //align your part
 318                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 319
 320                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 321
 322                                         for (int i = 1; i < processors; i++) {
 323                                                 bool tempResult;
 324                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 325                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 326                                         }
 327                                 }else{ //you are a child process
 328                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 329                                         MPIPos.resize(numFastaSeqs+1);
 330                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 331
 332
 333                                         //figure out how many sequences you have to align
 334                                         numSeqsPerProcessor = numFastaSeqs / processors;
 335                                         int startIndex =  pid * numSeqsPerProcessor;
 336                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 337
 338
 339                                         //align your part
 340                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 341
 342                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 343
 344                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 345                                 }
 346
 347                                 //close files
 348                                 MPI_File_close(&inMPI);
 349                                 MPI_File_close(&outMPIAlign);
 350                                 MPI_File_close(&outMPIReport);
 351                                 MPI_File_close(&outMPIAccnos);
 352
 353                                 //delete accnos file if blank
 354                                 if (pid == 0) {
 355                                         //delete accnos file if its blank else report to user
 356                                         if (MPIWroteAccnos) {
 357                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 358                                                 if (!flip) {
 359                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 360                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 361                                                 m->mothurOutEndLine();
 362                                         }else {
 363                                                 //MPI_Info info;
 364                                                 //MPI_File_delete(outAccnosFilename, info);
 365                                                 hasAccnos = false;
 366                                                 remove(accnosFileName.c_str());
 367                                         }
 368                                 }
 369
 370 #else
 371
 372         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 373                         if(processors == 1){
 374                                 ifstream inFASTA;
 375                                 openInputFile(candidateFileNames[s], inFASTA);
 376                                 getNumSeqs(inFASTA, numFastaSeqs);
 377                                 inFASTA.close();
 378
 379                                 lines.push_back(new linePair(0, numFastaSeqs));
 380
 381                                 driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 382
 383                                 if (m->control_pressed) {
 384                                         remove(accnosFileName.c_str());
 385                                         remove(alignFileName.c_str());
 386                                         remove(reportFileName.c_str());
 387                                         return 0;
 388                                 }
 389
 390                                 //delete accnos file if its blank else report to user
 391                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 392                                 else {
 393                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 394                                         if (!flip) {
 395                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 396                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 397                                         m->mothurOutEndLine();
 398                                 }
 399                         }
 400                         else{
 401                                 vector<int> positions;
 402                                 processIDS.resize(0);
 403
 404                                 ifstream inFASTA;
 405                                 openInputFile(candidateFileNames[s], inFASTA);
 406
 407                                 string input;
 408                                 while(!inFASTA.eof()){
 409                                         input = getline(inFASTA);
 410                                         if (input.length() != 0) {
 411                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 412                                         }
 413                                 }
 414                                 inFASTA.close();
 415
 416                                 numFastaSeqs = positions.size();
 417
 418                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 419
 420                                 for (int i = 0; i < processors; i++) {
 421                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 422                                         if(i == processors - 1){
 423                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 424                                         }
 425                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 426                                 }
 427
 428                                 createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 429
 430                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 431                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
 432
 433                                 //append alignment and report files
 434                                 for(int i=1;i<processors;i++){
 435                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 436                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 437
 438                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 439                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 440                                 }
 441
 442                                 vector<string> nonBlankAccnosFiles;
 443                                 //delete blank accnos files generated with multiple processes
 444                                 for(int i=0;i<processors;i++){
 445                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 446                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 447                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 448                                 }
 449
 450                                 //append accnos files
 451                                 if (nonBlankAccnosFiles.size() != 0) {
 452                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 453
 454                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 455                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
 456                                                 remove(nonBlankAccnosFiles[h].c_str());
 457                                         }
 458                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 459                                         if (!flip) {
 460                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 461                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 462                                         m->mothurOutEndLine();
 463                                 }else{ hasAccnos = false;  }
 464
 465                                 if (m->control_pressed) {
 466                                         remove(accnosFileName.c_str());
 467                                         remove(alignFileName.c_str());
 468                                         remove(reportFileName.c_str());
 469                                         return 0;
 470                                 }
 471                         }
 472         #else
 473                         ifstream inFASTA;
 474                         openInputFile(candidateFileNames[s], inFASTA);
 475                         getNumSeqs(inFASTA, numFastaSeqs);
 476                         inFASTA.close();
 477
 478                         lines.push_back(new linePair(0, numFastaSeqs));
 479
 480                         driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 481
 482                         if (m->control_pressed) {
 483                                 remove(accnosFileName.c_str());
 484                                 remove(alignFileName.c_str());
 485                                 remove(reportFileName.c_str());
 486                                 return 0;
 487                         }
 488
 489                         //delete accnos file if its blank else report to user
 490                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 491                         else {
 492                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 493                                 if (!flip) {
 494                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 495                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 496                                 m->mothurOutEndLine();
 497                         }
 498
 499         #endif
 500
 501 #endif
 502
 503
 504                 #ifdef USE_MPI
 505                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 506
 507                         if (pid == 0) { //only one process should output to screen
 508                 #endif
 509
 510                         outputNames.push_back(alignFileName);
 511                         outputNames.push_back(reportFileName);
 512                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);          }
 513
 514                 #ifdef USE_MPI
 515                         }
 516                 #endif
 517
 518                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 519                         m->mothurOutEndLine();
 520                         m->mothurOutEndLine();
 521                 }
 522
 523
 524                 m->mothurOutEndLine();
 525                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 526                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 527                 m->mothurOutEndLine();
 528
 529                 return 0;
 530         }
 531         catch(exception& e) {
 532                 m->errorOut(e, "AlignCommand", "execute");
 533                 exit(1);
 534         }
 535 }
 536
 537 //**********************************************************************************************************************
 538
 539 int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
 540         try {
 541                 ofstream alignmentFile;
 542                 openOutputFile(alignFName, alignmentFile);
 543
 544                 ofstream accnosFile;
 545                 openOutputFile(accnosFName, accnosFile);
 546
 547                 NastReport report(reportFName);
 548
 549                 ifstream inFASTA;
 550                 openInputFile(filename, inFASTA);
 551
 552                 inFASTA.seekg(line->start);
 553
 554                 for(int i=0;i<line->numSeqs;i++){
 555
 556                         if (m->control_pressed) {  return 0; }
 557
 558                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 559
 560                         int origNumBases = candidateSeq->getNumBases();
 561                         string originalUnaligned = candidateSeq->getUnaligned();
 562                         int numBasesNeeded = origNumBases * threshold;
 563
 564                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 565                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 566                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 567                                 }
 568
 569                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 570                                 Sequence* templateSeq = &temp;
 571
 572                                 float searchScore = templateDB->getSearchScore();
 573
 574                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 575                                 Sequence* copy;
 576
 577                                 Nast* nast2;
 578                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 579                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 580                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 581                                                                                                 //so this bool tells you if you need to delete it
 582
 583                                 //if there is a possibility that this sequence should be reversed
 584                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 585
 586                                         string wasBetter = "";
 587                                         //if the user wants you to try the reverse
 588                                         if (flip) {
 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                                                 }else{
 609                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 610                                                         delete nast2;
 611                                                         delete copy;
 612                                                 }
 613                                         }
 614
 615                                         //create accnos file with names
 616                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 617                                 }
 618
 619                                 report.setCandidate(candidateSeq);
 620                                 report.setTemplate(templateSeq);
 621                                 report.setSearchParameters(search, searchScore);
 622                                 report.setAlignmentParameters(align, alignment);
 623                                 report.setNastParameters(*nast);
 624
 625                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 626
 627                                 report.print();
 628                                 delete nast;
 629                                 if (needToDeleteCopy) {   delete copy;   }
 630                         }
 631                         delete candidateSeq;
 632
 633                         //report progress
 634                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 635                 }
 636                 //report progress
 637                 if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();           }
 638
 639                 alignmentFile.close();
 640                 inFASTA.close();
 641                 accnosFile.close();
 642
 643                 return 1;
 644         }
 645         catch(exception& e) {
 646                 m->errorOut(e, "AlignCommand", "driver");
 647                 exit(1);
 648         }
 649 }
 650 //**********************************************************************************************************************
 651 #ifdef USE_MPI
 652 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<long>& MPIPos){
 653         try {
 654                 string outputString = "";
 655                 MPI_Status statusReport;
 656                 MPI_Status statusAlign;
 657                 MPI_Status statusAccnos;
 658                 MPI_Status status;
 659                 int pid;
 660                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 661
 662                 NastReport report;
 663
 664                 if (pid == 0) {
 665                         outputString = report.getHeaders();
 666                         int length = outputString.length();
 667
 668                         char* buf = new char[length];
 669                         memcpy(buf, outputString.c_str(), length);
 670
 671                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 672
 673             delete buf;
 674                 }
 675
 676                 for(int i=0;i<num;i++){
 677
 678                         if (m->control_pressed) {  return 0; }
 679
 680                         //read next sequence
 681                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 682
 683                         char* buf4 = new char[length];
 684                         memcpy(buf4, outputString.c_str(), length);
 685
 686                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 687
 688                         string tempBuf = buf4;
 689
 690                         delete buf4;
 691
 692                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 693                         istringstream iss (tempBuf,istringstream::in);
 694
 695                         Sequence* candidateSeq = new Sequence(iss);
 696                         int origNumBases = candidateSeq->getNumBases();
 697                         string originalUnaligned = candidateSeq->getUnaligned();
 698                         int numBasesNeeded = origNumBases * threshold;
 699
 700                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 701                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 702                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 703                                 }
 704
 705                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 706                                 Sequence* templateSeq = &temp;
 707
 708                                 float searchScore = templateDB->getSearchScore();
 709
 710                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 711                                 Sequence* copy;
 712
 713                                 Nast* nast2;
 714                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 715                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 716                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 717                                                                                                 //so this bool tells you if you need to delete it
 718
 719                                 //if there is a possibility that this sequence should be reversed
 720                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 721
 722                                         string wasBetter = "";
 723                                         //if the user wants you to try the reverse
 724                                         if (flip) {
 725                                                 //get reverse compliment
 726                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 727                                                 copy->reverseComplement();
 728
 729                                                 //rerun alignment
 730                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 731                                                 Sequence* templateSeq2 = &temp2;
 732
 733                                                 searchScore = templateDB->getSearchScore();
 734
 735                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 736
 737                                                 //check if any better
 738                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 739                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 740                                                         templateSeq = templateSeq2;
 741                                                         delete nast;
 742                                                         nast = nast2;
 743                                                         needToDeleteCopy = true;
 744                                                 }else{
 745                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 746                                                         delete nast2;
 747                                                         delete copy;
 748                                                 }
 749                                         }
 750
 751                                         //create accnos file with names
 752                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 753
 754                                         //send results to parent
 755                                         int length = outputString.length();
 756
 757                                         char* buf = new char[length];
 758                                         memcpy(buf, outputString.c_str(), length);
 759
 760                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 761                                         delete buf;
 762                                         MPIWroteAccnos = true;
 763                                 }
 764
 765                                 report.setCandidate(candidateSeq);
 766                                 report.setTemplate(templateSeq);
 767                                 report.setSearchParameters(search, searchScore);
 768                                 report.setAlignmentParameters(align, alignment);
 769                                 report.setNastParameters(*nast);
 770
 771                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 772
 773                                 //send results to parent
 774                                 int length = outputString.length();
 775                                 char* buf2 = new char[length];
 776                                 memcpy(buf2, outputString.c_str(), length);
 777
 778                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 779
 780                                 delete buf2;
 781
 782                                 outputString = report.getReport();
 783
 784                                 //send results to parent
 785                                 length = outputString.length();
 786                                 char* buf3 = new char[length];
 787                                 memcpy(buf3, outputString.c_str(), length);
 788
 789                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 790
 791                                 delete buf3;
 792                                 delete nast;
 793                                 if (needToDeleteCopy) {   delete copy;   }
 794                         }
 795                         delete candidateSeq;
 796
 797                         //report progress
 798                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 799                 }
 800                 //report progress
 801                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 802
 803                 return 1;
 804         }
 805         catch(exception& e) {
 806                 m->errorOut(e, "AlignCommand", "driverMPI");
 807                 exit(1);
 808         }
 809 }
 810 #endif
 811 /**************************************************************************************************/
 812
 813 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 814         try {
 815 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 816                 int process = 0;
 817                 int exitCommand = 1;
 818                 //              processIDS.resize(0);
 819
 820                 //loop through and create all the processes you want
 821                 while (process != processors) {
 822                         int pid = fork();
 823
 824                         if (pid > 0) {
 825                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 826                                 process++;
 827                         }else if (pid == 0){
 828                                 exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 829                                 exit(0);
 830                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 831                 }
 832
 833                 //force parent to wait until all the processes are done
 834                 for (int i=0;i<processors;i++) {
 835                         int temp = processIDS[i];
 836                         wait(&temp);
 837                 }
 838
 839                 return exitCommand;
 840 #endif
 841         }
 842         catch(exception& e) {
 843                 m->errorOut(e, "AlignCommand", "createProcesses");
 844                 exit(1);
 845         }
 846 }
 847
 848 /**************************************************************************************************/
 849
 850 void AlignCommand::appendAlignFiles(string temp, string filename) {
 851         try{
 852
 853                 ofstream output;
 854                 ifstream input;
 855                 openOutputFileAppend(filename, output);
 856                 openInputFile(temp, input);
 857
 858                 while(char c = input.get()){
 859                         if(input.eof())         {       break;                  }
 860                         else                            {       output << c;    }
 861                 }
 862
 863                 input.close();
 864                 output.close();
 865         }
 866         catch(exception& e) {
 867                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 868                 exit(1);
 869         }
 870 }
 871 //**********************************************************************************************************************
 872
 873 void AlignCommand::appendReportFiles(string temp, string filename) {
 874         try{
 875
 876                 ofstream output;
 877                 ifstream input;
 878                 openOutputFileAppend(filename, output);
 879                 openInputFile(temp, input);
 880
 881                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 882
 883                 while(char c = input.get()){
 884                         if(input.eof())         {       break;                  }
 885                         else                            {       output << c;    }
 886                 }
 887
 888                 input.close();
 889                 output.close();
 890         }
 891         catch(exception& e) {
 892                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 893                 exit(1);
 894         }
 895 }
 896 //**********************************************************************************************************************