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[alignFileName.length()];
 271                                 strcpy(outAlignFilename, alignFileName.c_str());
 272
 273                                 char outReportFilename[reportFileName.length()];
 274                                 strcpy(outReportFilename, reportFileName.c_str());
 275
 276                                 char outAccnosFilename[accnosFileName.length()];
 277                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 278
 279                                 char inFileName[candidateFileNames[s].length()];
 280                                 strcpy(inFileName, candidateFileNames[s].c_str());
 281
 282                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 283                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 284                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 285                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 286
 287                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 288
 289                                 if (pid == 0) { //you are the root process
 290
 291                                         MPIPos = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 292
 293                                         //send file positions to all processes
 294                                         MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 295                                         MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 296
 297                                         //figure out how many sequences you have to align
 298                                         numSeqsPerProcessor = numFastaSeqs / processors;
 299                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 300                                         int startIndex =  pid * numSeqsPerProcessor;
 301
 302                                         //align your part
 303                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 304
 305                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 306
 307                                         for (int i = 1; i < processors; i++) {
 308                                                 bool tempResult;
 309                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 310                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 311                                         }
 312                                 }else{ //you are a child process
 313                                         MPI_Bcast(&numFastaSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 314                                         MPIPos.resize(numFastaSeqs+1);
 315                                         MPI_Bcast(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 316
 317                                         //figure out how many sequences you have to align
 318                                         numSeqsPerProcessor = numFastaSeqs / processors;
 319                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 320                                         int startIndex =  pid * numSeqsPerProcessor;
 321
 322                                         //align your part
 323                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 324
 325                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
 326
 327                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 328                                 }
 329
 330                                 //close files
 331                                 MPI_File_close(&inMPI);
 332                                 MPI_File_close(&outMPIAlign);
 333                                 MPI_File_close(&outMPIReport);
 334                                 MPI_File_close(&outMPIAccnos);
 335
 336                                 //delete accnos file if blank
 337                                 if (pid == 0) {
 338                                         //delete accnos file if its blank else report to user
 339                                         if (MPIWroteAccnos) {
 340                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 341                                                 if (!flip) {
 342                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 343                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 344                                                 m->mothurOutEndLine();
 345                                         }else {
 346                                                 //MPI_Info info;
 347                                                 //MPI_File_delete(outAccnosFilename, info);
 348                                                 hasAccnos = false;
 349                                                 remove(accnosFileName.c_str());
 350                                         }
 351                                 }
 352
 353 #else
 354
 355         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 356                         if(processors == 1){
 357                                 ifstream inFASTA;
 358                                 openInputFile(candidateFileNames[s], inFASTA);
 359                                 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 360                                 inFASTA.close();
 361
 362                                 lines.push_back(new linePair(0, numFastaSeqs));
 363
 364                                 driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 365
 366                                 if (m->control_pressed) {
 367                                         remove(accnosFileName.c_str());
 368                                         remove(alignFileName.c_str());
 369                                         remove(reportFileName.c_str());
 370                                         return 0;
 371                                 }
 372
 373                                 //delete accnos file if its blank else report to user
 374                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 375                                 else {
 376                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 377                                         if (!flip) {
 378                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 379                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 380                                         m->mothurOutEndLine();
 381                                 }
 382                         }
 383                         else{
 384                                 vector<int> positions;
 385                                 processIDS.resize(0);
 386
 387                                 ifstream inFASTA;
 388                                 openInputFile(candidateFileNames[s], inFASTA);
 389
 390                                 string input;
 391                                 while(!inFASTA.eof()){
 392                                         input = getline(inFASTA);
 393                                         if (input.length() != 0) {
 394                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 395                                         }
 396                                 }
 397                                 inFASTA.close();
 398
 399                                 numFastaSeqs = positions.size();
 400
 401                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 402
 403                                 for (int i = 0; i < processors; i++) {
 404                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 405                                         if(i == processors - 1){
 406                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 407                                         }
 408                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 409                                 }
 410
 411                                 createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 412
 413                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 414                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
 415
 416                                 //append alignment and report files
 417                                 for(int i=1;i<processors;i++){
 418                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 419                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 420
 421                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 422                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 423                                 }
 424
 425                                 vector<string> nonBlankAccnosFiles;
 426                                 //delete blank accnos files generated with multiple processes
 427                                 for(int i=0;i<processors;i++){
 428                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 429                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 430                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 431                                 }
 432
 433                                 //append accnos files
 434                                 if (nonBlankAccnosFiles.size() != 0) {
 435                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 436
 437                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 438                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
 439                                                 remove(nonBlankAccnosFiles[h].c_str());
 440                                         }
 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                                 }else{ hasAccnos = false;  }
 447
 448                                 if (m->control_pressed) {
 449                                         remove(accnosFileName.c_str());
 450                                         remove(alignFileName.c_str());
 451                                         remove(reportFileName.c_str());
 452                                         return 0;
 453                                 }
 454                         }
 455         #else
 456                         ifstream inFASTA;
 457                         openInputFile(candidateFileNames[s], inFASTA);
 458                         numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 459                         inFASTA.close();
 460
 461                         lines.push_back(new linePair(0, numFastaSeqs));
 462
 463                         driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 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                         //delete accnos file if its blank else report to user
 473                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 474                         else {
 475                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 476                                 if (!flip) {
 477                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 478                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 479                                 m->mothurOutEndLine();
 480                         }
 481
 482         #endif
 483
 484 #endif
 485
 486
 487                 #ifdef USE_MPI
 488                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 489
 490                         if (pid == 0) { //only one process should output to screen
 491                 #endif
 492
 493                         outputNames.push_back(alignFileName);
 494                         outputNames.push_back(reportFileName);
 495                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);          }
 496
 497                 #ifdef USE_MPI
 498                         }
 499                 #endif
 500
 501                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 502                         m->mothurOutEndLine();
 503                         m->mothurOutEndLine();
 504                 }
 505
 506
 507                 m->mothurOutEndLine();
 508                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 509                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 510                 m->mothurOutEndLine();
 511
 512                 return 0;
 513         }
 514         catch(exception& e) {
 515                 m->errorOut(e, "AlignCommand", "execute");
 516                 exit(1);
 517         }
 518 }
 519
 520 //**********************************************************************************************************************
 521
 522 int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
 523         try {
 524                 ofstream alignmentFile;
 525                 openOutputFile(alignFName, alignmentFile);
 526
 527                 ofstream accnosFile;
 528                 openOutputFile(accnosFName, accnosFile);
 529
 530                 NastReport report(reportFName);
 531
 532                 ifstream inFASTA;
 533                 openInputFile(filename, inFASTA);
 534
 535                 inFASTA.seekg(line->start);
 536
 537                 for(int i=0;i<line->numSeqs;i++){
 538
 539                         if (m->control_pressed) {  return 0; }
 540
 541                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 542
 543                         int origNumBases = candidateSeq->getNumBases();
 544                         string originalUnaligned = candidateSeq->getUnaligned();
 545                         int numBasesNeeded = origNumBases * threshold;
 546
 547                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 548                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 549                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 550                                 }
 551
 552                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 553                                 Sequence* templateSeq = &temp;
 554
 555                                 float searchScore = templateDB->getSearchScore();
 556
 557                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 558                                 Sequence* copy;
 559
 560                                 Nast* nast2;
 561                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 562                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 563                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 564                                                                                                 //so this bool tells you if you need to delete it
 565
 566                                 //if there is a possibility that this sequence should be reversed
 567                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 568
 569                                         string wasBetter = "";
 570                                         //if the user wants you to try the reverse
 571                                         if (flip) {
 572                                                 //get reverse compliment
 573                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 574                                                 copy->reverseComplement();
 575
 576                                                 //rerun alignment
 577                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 578                                                 Sequence* templateSeq2 = &temp2;
 579
 580                                                 searchScore = templateDB->getSearchScore();
 581
 582                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 583
 584                                                 //check if any better
 585                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 586                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 587                                                         templateSeq = templateSeq2;
 588                                                         delete nast;
 589                                                         nast = nast2;
 590                                                         needToDeleteCopy = true;
 591                                                 }else{
 592                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 593                                                         delete nast2;
 594                                                         delete copy;
 595                                                 }
 596                                         }
 597
 598                                         //create accnos file with names
 599                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 600                                 }
 601
 602                                 report.setCandidate(candidateSeq);
 603                                 report.setTemplate(templateSeq);
 604                                 report.setSearchParameters(search, searchScore);
 605                                 report.setAlignmentParameters(align, alignment);
 606                                 report.setNastParameters(*nast);
 607
 608                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 609
 610                                 report.print();
 611                                 delete nast;
 612                                 if (needToDeleteCopy) {   delete copy;   }
 613                         }
 614                         delete candidateSeq;
 615
 616                         //report progress
 617                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 618                 }
 619                 //report progress
 620                 if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();           }
 621
 622                 alignmentFile.close();
 623                 inFASTA.close();
 624                 accnosFile.close();
 625
 626                 return 1;
 627         }
 628         catch(exception& e) {
 629                 m->errorOut(e, "AlignCommand", "driver");
 630                 exit(1);
 631         }
 632 }
 633 //**********************************************************************************************************************
 634 #ifdef USE_MPI
 635 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<long>& MPIPos){
 636         try {
 637                 string outputString = "";
 638                 MPI_Status statusReport;
 639                 MPI_Status statusAlign;
 640                 MPI_Status statusAccnos;
 641                 MPI_Status status;
 642                 int pid;
 643                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 644
 645                 NastReport report;
 646
 647                 if (pid == 0) {
 648                         outputString = report.getHeaders();
 649                         int length = outputString.length();
 650                         char buf[length];
 651                         strcpy(buf, outputString.c_str());
 652
 653                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 654                 }
 655
 656                 for(int i=0;i<num;i++){
 657
 658                         if (m->control_pressed) {  return 0; }
 659
 660                         //read next sequence
 661                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 662                         char buf4[length];
 663                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 664
 665                         string tempBuf = buf4;
 666                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 667                         istringstream iss (tempBuf,istringstream::in);
 668
 669                         Sequence* candidateSeq = new Sequence(iss);
 670                         int origNumBases = candidateSeq->getNumBases();
 671                         string originalUnaligned = candidateSeq->getUnaligned();
 672                         int numBasesNeeded = origNumBases * threshold;
 673
 674                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 675                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 676                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 677                                 }
 678
 679                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 680                                 Sequence* templateSeq = &temp;
 681
 682                                 float searchScore = templateDB->getSearchScore();
 683
 684                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 685                                 Sequence* copy;
 686
 687                                 Nast* nast2;
 688                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 689                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 690                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 691                                                                                                 //so this bool tells you if you need to delete it
 692
 693                                 //if there is a possibility that this sequence should be reversed
 694                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 695
 696                                         string wasBetter = "";
 697                                         //if the user wants you to try the reverse
 698                                         if (flip) {
 699                                                 //get reverse compliment
 700                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 701                                                 copy->reverseComplement();
 702
 703                                                 //rerun alignment
 704                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 705                                                 Sequence* templateSeq2 = &temp2;
 706
 707                                                 searchScore = templateDB->getSearchScore();
 708
 709                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 710
 711                                                 //check if any better
 712                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 713                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 714                                                         templateSeq = templateSeq2;
 715                                                         delete nast;
 716                                                         nast = nast2;
 717                                                         needToDeleteCopy = true;
 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                                         char buf[length];
 731                                         strcpy(buf, outputString.c_str());
 732
 733                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 734                                         MPIWroteAccnos = true;
 735                                 }
 736
 737                                 report.setCandidate(candidateSeq);
 738                                 report.setTemplate(templateSeq);
 739                                 report.setSearchParameters(search, searchScore);
 740                                 report.setAlignmentParameters(align, alignment);
 741                                 report.setNastParameters(*nast);
 742
 743                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 744
 745                                 //send results to parent
 746                                 int length = outputString.length();
 747                                 char buf2[length];
 748                                 strcpy(buf2, outputString.c_str());
 749
 750                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 751
 752                                 outputString = report.getReport();
 753
 754                                 //send results to parent
 755                                 length = outputString.length();
 756                                 char buf3[length];
 757                                 strcpy(buf3, outputString.c_str());
 758
 759                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 760
 761                                 delete nast;
 762                                 if (needToDeleteCopy) {   delete copy;   }
 763                         }
 764                         delete candidateSeq;
 765
 766                         //report progress
 767                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 768                 }
 769                 //report progress
 770                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 771
 772                 return 1;
 773         }
 774         catch(exception& e) {
 775                 m->errorOut(e, "AlignCommand", "driverMPI");
 776                 exit(1);
 777         }
 778 }
 779 #endif
 780 /**************************************************************************************************/
 781
 782 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 783         try {
 784 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 785                 int process = 0;
 786                 int exitCommand = 1;
 787                 //              processIDS.resize(0);
 788
 789                 //loop through and create all the processes you want
 790                 while (process != processors) {
 791                         int pid = fork();
 792
 793                         if (pid > 0) {
 794                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 795                                 process++;
 796                         }else if (pid == 0){
 797                                 exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 798                                 exit(0);
 799                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 800                 }
 801
 802                 //force parent to wait until all the processes are done
 803                 for (int i=0;i<processors;i++) {
 804                         int temp = processIDS[i];
 805                         wait(&temp);
 806                 }
 807
 808                 return exitCommand;
 809 #endif
 810         }
 811         catch(exception& e) {
 812                 m->errorOut(e, "AlignCommand", "createProcesses");
 813                 exit(1);
 814         }
 815 }
 816
 817 /**************************************************************************************************/
 818
 819 void AlignCommand::appendAlignFiles(string temp, string filename) {
 820         try{
 821
 822                 ofstream output;
 823                 ifstream input;
 824                 openOutputFileAppend(filename, output);
 825                 openInputFile(temp, input);
 826
 827                 while(char c = input.get()){
 828                         if(input.eof())         {       break;                  }
 829                         else                            {       output << c;    }
 830                 }
 831
 832                 input.close();
 833                 output.close();
 834         }
 835         catch(exception& e) {
 836                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 837                 exit(1);
 838         }
 839 }
 840 //**********************************************************************************************************************
 841
 842 void AlignCommand::appendReportFiles(string temp, string filename) {
 843         try{
 844
 845                 ofstream output;
 846                 ifstream input;
 847                 openOutputFileAppend(filename, output);
 848                 openInputFile(temp, input);
 849
 850                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 851
 852                 while(char c = input.get()){
 853                         if(input.eof())         {       break;                  }
 854                         else                            {       output << c;    }
 855                 }
 856
 857                 input.close();
 858                 output.close();
 859         }
 860         catch(exception& e) {
 861                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 862                 exit(1);
 863         }
 864 }
 865 //**********************************************************************************************************************