aligncommand.cpp

   1 /*
   2  *  aligncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/15/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  *      This version of nast does everything I think that the greengenes nast server does and then some.  I have added the
   9  *      feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
  10  *      method.  This latter feature is perhaps most significant.  nastPlus enables a user to use either a Needleman-Wunsch
  11  *      (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm.  This is significant because it
  12  *      allows for a global alignment and not the local alignment provided by bLAst.  Furthermore, it has the potential to
  13  *      provide a better alignment because of the banding method employed by blast (I'm not sure about this).
  14  *
  15  */
  16
  17 #include "aligncommand.h"
  18 #include "sequence.hpp"
  19
  20 #include "gotohoverlap.hpp"
  21 #include "needlemanoverlap.hpp"
  22 #include "blastalign.hpp"
  23 #include "noalign.hpp"
  24
  25 #include "nast.hpp"
  26 #include "nastreport.hpp"
  27
  28
  29 //**********************************************************************************************************************
  30 vector<string> AlignCommand::getValidParameters(){
  31         try {
  32                 string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
  33                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "AlignCommand", "getValidParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 vector<string> AlignCommand::getRequiredParameters(){
  43         try {
  44                 string AlignArray[] =  {"template","candidate"};
  45                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  46                 return myArray;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "AlignCommand", "getRequiredParameters");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 vector<string> AlignCommand::getRequiredFiles(){
  55         try {
  56                 vector<string> myArray;
  57                 return myArray;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "AlignCommand", "getRequiredFiles");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 AlignCommand::AlignCommand(){
  66         try {
  67                 abort = true; calledHelp = true;
  68                 vector<string> tempOutNames;
  69                 outputTypes["fasta"] = tempOutNames;
  70                 outputTypes["alignreport"] = tempOutNames;
  71                 outputTypes["accnos"] = tempOutNames;
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "AlignCommand", "AlignCommand");
  75                 exit(1);
  76         }
  77 }
  78 //**********************************************************************************************************************
  79 AlignCommand::AlignCommand(string option)  {
  80         try {
  81                 abort = false; calledHelp = false;
  82                 currentFiles = CurrentFile::getInstance();
  83
  84                 //allow user to run help
  85                 if(option == "help") { help(); abort = true; calledHelp = true;}
  86
  87                 else {
  88
  89                         //valid paramters for this command
  90                         string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
  91                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  92
  93                         OptionParser parser(option);
  94                         map<string, string> parameters = parser.getParameters();
  95
  96                         ValidParameters validParameter("align.seqs");
  97                         map<string, string>::iterator it;
  98
  99                         //check to make sure all parameters are valid for command
 100                         for (it = parameters.begin(); it != parameters.end(); it++) {
 101                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 102                         }
 103
 104                         //initialize outputTypes
 105                         vector<string> tempOutNames;
 106                         outputTypes["fasta"] = tempOutNames;
 107                         outputTypes["alignreport"] = tempOutNames;
 108                         outputTypes["accnos"] = tempOutNames;
 109
 110                         //if the user changes the output directory command factory will send this info to us in the output parameter
 111                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 112
 113
 114                         //if the user changes the input directory command factory will send this info to us in the output parameter
 115                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 116
 117                         if (inputDir == "not found"){   inputDir = "";          }
 118                         else {
 119                                 string path;
 120
 121                                 it = parameters.find("template");
 122
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
 128                                 }
 129                         }
 130
 131                         //check for required parameters
 132                         templateFileName = validParameter.validFile(parameters, "template", true);
 133
 134                         if (templateFileName == "not found") {
 135                                 m->mothurOut("template is a required parameter for the align.seqs command.");
 136                                 m->mothurOutEndLine();
 137                                 abort = true;
 138                         }else if (templateFileName == "not open") { abort = true; }
 139
 140                         candidateFileName = validParameter.validFile(parameters, "candidate", false);
 141                         if (candidateFileName == "not found") {
 142                                 //check currentFiles for a fasta file
 143                                 if (currentFiles->getFastaFile() != "") {  candidateFileName = currentFiles->getFastaFile(); m->mothurOut("Using " + candidateFileName + " as candidate file."); m->mothurOutEndLine();
 144                                 }else { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true;  }
 145                         }else {
 146                                 m->splitAtDash(candidateFileName, candidateFileNames);
 147
 148                                 //go through files and make sure they are good, if not, then disregard them
 149                                 for (int i = 0; i < candidateFileNames.size(); i++) {
 150                                         //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
 151
 152                                         if (inputDir != "") {
 153                                                 string path = m->hasPath(candidateFileNames[i]);
 154                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 155                                                 if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
 156                                         }
 157
 158                                         int ableToOpen;
 159                                         ifstream in;
 160                                         ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
 161                                         in.close();
 162
 163                                         //if you can't open it, try default location
 164                                         if (ableToOpen == 1) {
 165                                                 if (m->getDefaultPath() != "") { //default path is set
 166                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
 167                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 168                                                         ifstream in2;
 169                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 170                                                         in2.close();
 171                                                         candidateFileNames[i] = tryPath;
 172                                                 }
 173                                         }
 174
 175                                         //if you can't open it, try output location
 176                                         if (ableToOpen == 1) {
 177                                                 if (m->getOutputDir() != "") { //default path is set
 178                                                         string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
 179                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 180                                                         ifstream in2;
 181                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 182                                                         in2.close();
 183                                                         candidateFileNames[i] = tryPath;
 184                                                 }
 185                                         }
 186
 187
 188
 189                                         if (ableToOpen == 1) {
 190                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 191                                                 //erase from file list
 192                                                 candidateFileNames.erase(candidateFileNames.begin()+i);
 193                                                 i--;
 194                                         }
 195
 196                                 }
 197
 198                                 //make sure there is at least one valid file left
 199                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 200                         }
 201
 202                         //check for optional parameter and set defaults
 203                         // ...at some point should added some additional type checking...
 204                         string temp;
 205                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 206                         convert(temp, kmerSize);
 207
 208                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 209                         convert(temp, match);
 210
 211                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 212                         convert(temp, misMatch);
 213
 214                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 215                         convert(temp, gapOpen);
 216
 217                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 218                         convert(temp, gapExtend);
 219
 220                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 221                         convert(temp, processors);
 222
 223                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 224                         flip = m->isTrue(temp);
 225
 226                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 227                         convert(temp, threshold);
 228
 229                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 230
 231                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 232                 }
 233
 234         }
 235         catch(exception& e) {
 236                 m->errorOut(e, "AlignCommand", "AlignCommand");
 237                 exit(1);
 238         }
 239 }
 240 //**********************************************************************************************************************
 241
 242 AlignCommand::~AlignCommand(){
 243
 244         if (abort == false) {
 245                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 246                 delete templateDB;
 247                 delete alignment;
 248         }
 249 }
 250
 251 //**********************************************************************************************************************
 252
 253 void AlignCommand::help(){
 254         try {
 255                 m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
 256                 m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen, gapextend and processors.\n");
 257                 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");
 258                 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");
 259                 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");
 260                 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 261                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 262                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 263                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 264                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 265                 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");
 266                 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");
 267                 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");
 268                 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");
 269                 m->mothurOut("The align.seqs command should be in the following format: \n");
 270                 m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
 271                 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");
 272                 m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
 273         }
 274         catch(exception& e) {
 275                 m->errorOut(e, "AlignCommand", "help");
 276                 exit(1);
 277         }
 278 }
 279
 280
 281 //**********************************************************************************************************************
 282
 283 int AlignCommand::execute(){
 284         try {
 285                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 286
 287                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 288                 int longestBase = templateDB->getLongestBase();
 289
 290                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 291                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 292                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 293                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 294                 else {
 295                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 296                         m->mothurOutEndLine();
 297                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 298                 }
 299
 300                 for (int s = 0; s < candidateFileNames.size(); s++) {
 301                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 302
 303                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 304
 305                         if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
 306                         string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
 307                         string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
 308                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
 309                         bool hasAccnos = true;
 310
 311                         int numFastaSeqs = 0;
 312                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 313                         int start = time(NULL);
 314
 315 #ifdef USE_MPI
 316                                 int pid, numSeqsPerProcessor;
 317                                 int tag = 2001;
 318                                 vector<unsigned long int> MPIPos;
 319                                 MPIWroteAccnos = false;
 320
 321                                 MPI_Status status;
 322                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 323                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 324
 325                                 MPI_File inMPI;
 326                                 MPI_File outMPIAlign;
 327                                 MPI_File outMPIReport;
 328                                 MPI_File outMPIAccnos;
 329
 330                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 331                                 int inMode=MPI_MODE_RDONLY;
 332
 333                                 char outAlignFilename[1024];
 334                                 strcpy(outAlignFilename, alignFileName.c_str());
 335
 336                                 char outReportFilename[1024];
 337                                 strcpy(outReportFilename, reportFileName.c_str());
 338
 339                                 char outAccnosFilename[1024];
 340                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 341
 342                                 char inFileName[1024];
 343                                 strcpy(inFileName, candidateFileNames[s].c_str());
 344
 345                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 346                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 347                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 348                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 349
 350                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 351
 352                                 if (pid == 0) { //you are the root process
 353
 354                                         MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 355
 356                                         //send file positions to all processes
 357                                         for(int i = 1; i < processors; i++) {
 358                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 359                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 360                                         }
 361
 362                                         //figure out how many sequences you have to align
 363                                         numSeqsPerProcessor = numFastaSeqs / processors;
 364                                         int startIndex =  pid * numSeqsPerProcessor;
 365                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 366
 367                                         //align your part
 368                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 369
 370                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 371
 372                                         for (int i = 1; i < processors; i++) {
 373                                                 bool tempResult;
 374                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 375                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 376                                         }
 377                                 }else{ //you are a child process
 378                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 379                                         MPIPos.resize(numFastaSeqs+1);
 380                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 381
 382
 383                                         //figure out how many sequences you have to align
 384                                         numSeqsPerProcessor = numFastaSeqs / processors;
 385                                         int startIndex =  pid * numSeqsPerProcessor;
 386                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 387
 388
 389                                         //align your part
 390                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 391
 392                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 393
 394                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 395                                 }
 396
 397                                 //close files
 398                                 MPI_File_close(&inMPI);
 399                                 MPI_File_close(&outMPIAlign);
 400                                 MPI_File_close(&outMPIReport);
 401                                 MPI_File_close(&outMPIAccnos);
 402
 403                                 //delete accnos file if blank
 404                                 if (pid == 0) {
 405                                         //delete accnos file if its blank else report to user
 406                                         if (MPIWroteAccnos) {
 407                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 408                                                 if (!flip) {
 409                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 410                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 411                                                 m->mothurOutEndLine();
 412                                         }else {
 413                                                 //MPI_Info info;
 414                                                 //MPI_File_delete(outAccnosFilename, info);
 415                                                 hasAccnos = false;
 416                                                 remove(accnosFileName.c_str());
 417                                         }
 418                                 }
 419
 420 #else
 421
 422                 vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
 423                 for (int i = 0; i < (positions.size()-1); i++) {
 424                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 425                 }
 426         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 427                         if(processors == 1){
 428                                 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 429                         }else{
 430                                 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 431                         }
 432         #else
 433                         numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 434         #endif
 435
 436                         if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear();  return 0; }
 437
 438                         //delete accnos file if its blank else report to user
 439                         if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 440                         else {
 441                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 442                                 if (!flip) {
 443                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 444                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 445                                 m->mothurOutEndLine();
 446                         }
 447
 448 #endif
 449
 450
 451                 #ifdef USE_MPI
 452                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 453
 454                         if (pid == 0) { //only one process should output to screen
 455                 #endif
 456
 457                         outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
 458                         outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
 459                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);  }
 460
 461                 #ifdef USE_MPI
 462                         }
 463                 #endif
 464
 465                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 466                         m->mothurOutEndLine();
 467                         m->mothurOutEndLine();
 468                 }
 469
 470                 //set align file as new current fastafile
 471                 string currentFasta = "";
 472                 itTypes = outputTypes.find("fasta");
 473                 if (itTypes != outputTypes.end()) {
 474                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; }
 475                 }
 476                 currentFiles->setFastaFile(currentFasta);
 477                 cout << "current fasta = " << currentFiles->getFastaFile() << endl;
 478                 m->mothurOutEndLine();
 479                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 480                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 481                 m->mothurOutEndLine();
 482
 483                 return 0;
 484         }
 485         catch(exception& e) {
 486                 m->errorOut(e, "AlignCommand", "execute");
 487                 exit(1);
 488         }
 489 }
 490
 491 //**********************************************************************************************************************
 492
 493 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
 494         try {
 495                 ofstream alignmentFile;
 496                 m->openOutputFile(alignFName, alignmentFile);
 497
 498                 ofstream accnosFile;
 499                 m->openOutputFile(accnosFName, accnosFile);
 500
 501                 NastReport report(reportFName);
 502
 503                 ifstream inFASTA;
 504                 m->openInputFile(filename, inFASTA);
 505
 506                 inFASTA.seekg(filePos->start);
 507
 508                 bool done = false;
 509                 int count = 0;
 510
 511                 while (!done) {
 512
 513                         if (m->control_pressed) {  return 0; }
 514
 515                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 516                         report.setCandidate(candidateSeq);
 517
 518                         int origNumBases = candidateSeq->getNumBases();
 519                         string originalUnaligned = candidateSeq->getUnaligned();
 520                         int numBasesNeeded = origNumBases * threshold;
 521
 522                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 523                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 524                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 525                                 }
 526
 527                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 528                                 Sequence* templateSeq = &temp;
 529
 530                                 float searchScore = templateDB->getSearchScore();
 531
 532                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 533
 534                                 Sequence* copy;
 535
 536                                 Nast* nast2;
 537                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 538                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 539                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 540                                                                                                 //so this bool tells you if you need to delete it
 541
 542                                 //if there is a possibility that this sequence should be reversed
 543                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 544
 545                                         string wasBetter =  "";
 546                                         //if the user wants you to try the reverse
 547                                         if (flip) {
 548
 549                                                 //get reverse compliment
 550                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 551                                                 copy->reverseComplement();
 552
 553                                                 //rerun alignment
 554                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 555                                                 Sequence* templateSeq2 = &temp2;
 556
 557                                                 searchScore = templateDB->getSearchScore();
 558
 559                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 560
 561                                                 //check if any better
 562                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 563                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 564                                                         templateSeq = templateSeq2;
 565                                                         delete nast;
 566                                                         nast = nast2;
 567                                                         needToDeleteCopy = true;
 568                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 569                                                 }else{
 570                                                         wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 571                                                         delete nast2;
 572                                                         delete copy;
 573                                                 }
 574                                         }
 575
 576                                         //create accnos file with names
 577                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 578                                 }
 579
 580                                 report.setTemplate(templateSeq);
 581                                 report.setSearchParameters(search, searchScore);
 582                                 report.setAlignmentParameters(align, alignment);
 583                                 report.setNastParameters(*nast);
 584
 585                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 586
 587                                 report.print();
 588                                 delete nast;
 589                                 if (needToDeleteCopy) {   delete copy;   }
 590
 591                                 count++;
 592                         }
 593                         delete candidateSeq;
 594
 595                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 596                                 unsigned long int pos = inFASTA.tellg();
 597                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 598                         #else
 599                                 if (inFASTA.eof()) { break; }
 600                         #endif
 601
 602                         //report progress
 603                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 604
 605                 }
 606                 //report progress
 607                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 608
 609                 alignmentFile.close();
 610                 inFASTA.close();
 611                 accnosFile.close();
 612
 613                 return count;
 614         }
 615         catch(exception& e) {
 616                 m->errorOut(e, "AlignCommand", "driver");
 617                 exit(1);
 618         }
 619 }
 620 //**********************************************************************************************************************
 621 #ifdef USE_MPI
 622 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
 623         try {
 624                 string outputString = "";
 625                 MPI_Status statusReport;
 626                 MPI_Status statusAlign;
 627                 MPI_Status statusAccnos;
 628                 MPI_Status status;
 629                 int pid;
 630                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 631
 632                 NastReport report;
 633
 634                 if (pid == 0) {
 635                         outputString = report.getHeaders();
 636                         int length = outputString.length();
 637
 638                         char* buf = new char[length];
 639                         memcpy(buf, outputString.c_str(), length);
 640
 641                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 642
 643             delete buf;
 644                 }
 645
 646                 for(int i=0;i<num;i++){
 647
 648                         if (m->control_pressed) {  return 0; }
 649
 650                         //read next sequence
 651                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 652
 653                         char* buf4 = new char[length];
 654                         //memcpy(buf4, outputString.c_str(), length);
 655
 656                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 657
 658                         string tempBuf = buf4;
 659
 660                         delete buf4;
 661
 662                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 663
 664                         istringstream iss (tempBuf,istringstream::in);
 665
 666                         Sequence* candidateSeq = new Sequence(iss);
 667                         report.setCandidate(candidateSeq);
 668
 669                         int origNumBases = candidateSeq->getNumBases();
 670                         string originalUnaligned = candidateSeq->getUnaligned();
 671                         int numBasesNeeded = origNumBases * threshold;
 672
 673                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 674                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 675                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 676                                 }
 677
 678                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 679                                 Sequence* templateSeq = &temp;
 680
 681                                 float searchScore = templateDB->getSearchScore();
 682
 683                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 684                                 Sequence* copy;
 685
 686                                 Nast* nast2;
 687                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 688                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 689                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 690                                                                                                 //so this bool tells you if you need to delete it
 691
 692                                 //if there is a possibility that this sequence should be reversed
 693                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 694
 695                                         string wasBetter = "";
 696                                         //if the user wants you to try the reverse
 697                                         if (flip) {
 698                                                 //get reverse compliment
 699                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 700                                                 copy->reverseComplement();
 701
 702                                                 //rerun alignment
 703                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 704                                                 Sequence* templateSeq2 = &temp2;
 705
 706                                                 searchScore = templateDB->getSearchScore();
 707
 708                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 709
 710                                                 //check if any better
 711                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 712                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 713                                                         templateSeq = templateSeq2;
 714                                                         delete nast;
 715                                                         nast = nast2;
 716                                                         needToDeleteCopy = true;
 717                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 718                                                 }else{
 719                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 720                                                         delete nast2;
 721                                                         delete copy;
 722                                                 }
 723                                         }
 724
 725                                         //create accnos file with names
 726                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 727
 728                                         //send results to parent
 729                                         int length = outputString.length();
 730
 731                                         char* buf = new char[length];
 732                                         memcpy(buf, outputString.c_str(), length);
 733
 734                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 735                                         delete buf;
 736                                         MPIWroteAccnos = true;
 737                                 }
 738
 739                                 report.setTemplate(templateSeq);
 740                                 report.setSearchParameters(search, searchScore);
 741                                 report.setAlignmentParameters(align, alignment);
 742                                 report.setNastParameters(*nast);
 743
 744                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 745
 746                                 //send results to parent
 747                                 int length = outputString.length();
 748                                 char* buf2 = new char[length];
 749                                 memcpy(buf2, outputString.c_str(), length);
 750
 751                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 752
 753                                 delete buf2;
 754
 755                                 outputString = report.getReport();
 756
 757                                 //send results to parent
 758                                 length = outputString.length();
 759                                 char* buf3 = new char[length];
 760                                 memcpy(buf3, outputString.c_str(), length);
 761
 762                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 763
 764                                 delete buf3;
 765                                 delete nast;
 766                                 if (needToDeleteCopy) {   delete copy;   }
 767                         }
 768                         delete candidateSeq;
 769
 770                         //report progress
 771                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 772                 }
 773                 //report progress
 774                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 775
 776                 return 1;
 777         }
 778         catch(exception& e) {
 779                 m->errorOut(e, "AlignCommand", "driverMPI");
 780                 exit(1);
 781         }
 782 }
 783 #endif
 784 /**************************************************************************************************/
 785
 786 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 787         try {
 788 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 789                 processIDS.resize(0);
 790                 int process = 1;
 791                 int num = 0;
 792                 //              processIDS.resize(0);
 793
 794                 //loop through and create all the processes you want
 795                 while (process != processors) {
 796                         int pid = fork();
 797
 798                         if (pid > 0) {
 799                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 800                                 process++;
 801                         }else if (pid == 0){
 802                                 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 803
 804                                 //pass numSeqs to parent
 805                                 ofstream out;
 806                                 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
 807                                 m->openOutputFile(tempFile, out);
 808                                 out << num << endl;
 809                                 out.close();
 810
 811                                 exit(0);
 812                         }else {
 813                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 814                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 815                                 exit(0);
 816                         }
 817                 }
 818
 819                 //do my part
 820                 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
 821
 822                 //force parent to wait until all the processes are done
 823                 for (int i=0;i<processors;i++) {
 824                         int temp = processIDS[i];
 825                         wait(&temp);
 826                 }
 827
 828                 vector<string> nonBlankAccnosFiles;
 829                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 830                 else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it
 831
 832                 for (int i = 0; i < processIDS.size(); i++) {
 833                         ifstream in;
 834                         string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
 835                         m->openInputFile(tempFile, in);
 836                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 837                         in.close(); remove(tempFile.c_str());
 838
 839                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 840                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 841
 842                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 843                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 844
 845                         if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
 846                                 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
 847                         }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str());  }
 848
 849                 }
 850
 851                 //append accnos files
 852                 if (nonBlankAccnosFiles.size() != 0) {
 853                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 854
 855                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 856                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
 857                                 remove(nonBlankAccnosFiles[h].c_str());
 858                         }
 859                 }else { //recreate the accnosfile if needed
 860                         ofstream out;
 861                         m->openOutputFile(accnosFName, out);
 862                         out.close();
 863                 }
 864
 865                 return num;
 866 #endif
 867         }
 868         catch(exception& e) {
 869                 m->errorOut(e, "AlignCommand", "createProcesses");
 870                 exit(1);
 871         }
 872 }
 873 /**************************************************************************************************/
 874
 875 void AlignCommand::appendAlignFiles(string temp, string filename) {
 876         try{
 877
 878                 ofstream output;
 879                 ifstream input;
 880                 m->openOutputFileAppend(filename, output);
 881                 m->openInputFile(temp, input);
 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", "appendAlignFiles");
 893                 exit(1);
 894         }
 895 }
 896 //**********************************************************************************************************************
 897
 898 void AlignCommand::appendReportFiles(string temp, string filename) {
 899         try{
 900
 901                 ofstream output;
 902                 ifstream input;
 903                 m->openOutputFileAppend(filename, output);
 904                 m->openInputFile(temp, input);
 905
 906                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 907
 908                 while(char c = input.get()){
 909                         if(input.eof())         {       break;                  }
 910                         else                            {       output << c;    }
 911                 }
 912
 913                 input.close();
 914                 output.close();
 915         }
 916         catch(exception& e) {
 917                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 918                 exit(1);
 919         }
 920 }
 921 //**********************************************************************************************************************