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;
  68                 //initialize outputTypes
  69                 vector<string> tempOutNames;
  70                 outputTypes["fasta"] = tempOutNames;
  71                 outputTypes["alignreport"] = tempOutNames;
  72                 outputTypes["accnos"] = tempOutNames;
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "AlignCommand", "AlignCommand");
  76                 exit(1);
  77         }
  78 }
  79 //**********************************************************************************************************************
  80 AlignCommand::AlignCommand(string option)  {
  81         try {
  82                 abort = false;
  83
  84                 //allow user to run help
  85                 if(option == "help") { help(); abort = 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") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true;  }
 142                         else {
 143                                 m->splitAtDash(candidateFileName, candidateFileNames);
 144
 145                                 //go through files and make sure they are good, if not, then disregard them
 146                                 for (int i = 0; i < candidateFileNames.size(); i++) {
 147                                         //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
 148
 149                                         if (inputDir != "") {
 150                                                 string path = m->hasPath(candidateFileNames[i]);
 151                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 152                                                 if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
 153                                         }
 154
 155                                         int ableToOpen;
 156                                         ifstream in;
 157                                         ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
 158                                         in.close();
 159
 160                                         //if you can't open it, try default location
 161                                         if (ableToOpen == 1) {
 162                                                 if (m->getDefaultPath() != "") { //default path is set
 163                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
 164                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 165                                                         ifstream in2;
 166                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 167                                                         in2.close();
 168                                                         candidateFileNames[i] = tryPath;
 169                                                 }
 170                                         }
 171
 172                                         //if you can't open it, try default location
 173                                         if (ableToOpen == 1) {
 174                                                 if (m->getOutputDir() != "") { //default path is set
 175                                                         string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
 176                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 177                                                         ifstream in2;
 178                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 179                                                         in2.close();
 180                                                         candidateFileNames[i] = tryPath;
 181                                                 }
 182                                         }
 183
 184
 185
 186                                         if (ableToOpen == 1) {
 187                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 188                                                 //erase from file list
 189                                                 candidateFileNames.erase(candidateFileNames.begin()+i);
 190                                                 i--;
 191                                         }
 192
 193                                 }
 194
 195                                 //make sure there is at least one valid file left
 196                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 197                         }
 198
 199                         //check for optional parameter and set defaults
 200                         // ...at some point should added some additional type checking...
 201                         string temp;
 202                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 203                         convert(temp, kmerSize);
 204
 205                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 206                         convert(temp, match);
 207
 208                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 209                         convert(temp, misMatch);
 210
 211                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 212                         convert(temp, gapOpen);
 213
 214                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 215                         convert(temp, gapExtend);
 216
 217                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 218                         convert(temp, processors);
 219
 220                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 221                         flip = m->isTrue(temp);
 222
 223                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 224                         convert(temp, threshold);
 225
 226                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 227
 228                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 229                 }
 230
 231         }
 232         catch(exception& e) {
 233                 m->errorOut(e, "AlignCommand", "AlignCommand");
 234                 exit(1);
 235         }
 236 }
 237 //**********************************************************************************************************************
 238
 239 AlignCommand::~AlignCommand(){
 240
 241         if (abort == false) {
 242                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 243                 delete templateDB;
 244                 delete alignment;
 245         }
 246 }
 247
 248 //**********************************************************************************************************************
 249
 250 void AlignCommand::help(){
 251         try {
 252                 m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
 253                 m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen, gapextend and processors.\n");
 254                 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");
 255                 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");
 256                 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");
 257                 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 258                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 259                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 260                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 261                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 262                 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");
 263                 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");
 264                 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");
 265                 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");
 266                 m->mothurOut("The align.seqs command should be in the following format: \n");
 267                 m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
 268                 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");
 269                 m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
 270         }
 271         catch(exception& e) {
 272                 m->errorOut(e, "AlignCommand", "help");
 273                 exit(1);
 274         }
 275 }
 276
 277
 278 //**********************************************************************************************************************
 279
 280 int AlignCommand::execute(){
 281         try {
 282                 if (abort == true) { return 0;  }
 283
 284                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 285                 int longestBase = templateDB->getLongestBase();
 286
 287                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 288                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 289                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 290                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 291                 else {
 292                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 293                         m->mothurOutEndLine();
 294                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 295                 }
 296
 297                 for (int s = 0; s < candidateFileNames.size(); s++) {
 298                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 299
 300                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 301
 302                         if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
 303                         string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
 304                         string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
 305                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
 306                         bool hasAccnos = true;
 307
 308                         int numFastaSeqs = 0;
 309                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 310                         int start = time(NULL);
 311
 312 #ifdef USE_MPI
 313                                 int pid, numSeqsPerProcessor;
 314                                 int tag = 2001;
 315                                 vector<unsigned long int> MPIPos;
 316                                 MPIWroteAccnos = false;
 317
 318                                 MPI_Status status;
 319                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 320                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 321
 322                                 MPI_File inMPI;
 323                                 MPI_File outMPIAlign;
 324                                 MPI_File outMPIReport;
 325                                 MPI_File outMPIAccnos;
 326
 327                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 328                                 int inMode=MPI_MODE_RDONLY;
 329
 330                                 char outAlignFilename[1024];
 331                                 strcpy(outAlignFilename, alignFileName.c_str());
 332
 333                                 char outReportFilename[1024];
 334                                 strcpy(outReportFilename, reportFileName.c_str());
 335
 336                                 char outAccnosFilename[1024];
 337                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 338
 339                                 char inFileName[1024];
 340                                 strcpy(inFileName, candidateFileNames[s].c_str());
 341
 342                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 343                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 344                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 345                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 346
 347                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 348
 349                                 if (pid == 0) { //you are the root process
 350
 351                                         MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 352
 353                                         //send file positions to all processes
 354                                         for(int i = 1; i < processors; i++) {
 355                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 356                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 357                                         }
 358
 359                                         //figure out how many sequences you have to align
 360                                         numSeqsPerProcessor = numFastaSeqs / processors;
 361                                         int startIndex =  pid * numSeqsPerProcessor;
 362                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 363
 364                                         //align your part
 365                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 366
 367                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 368
 369                                         for (int i = 1; i < processors; i++) {
 370                                                 bool tempResult;
 371                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 372                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 373                                         }
 374                                 }else{ //you are a child process
 375                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 376                                         MPIPos.resize(numFastaSeqs+1);
 377                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 378
 379
 380                                         //figure out how many sequences you have to align
 381                                         numSeqsPerProcessor = numFastaSeqs / processors;
 382                                         int startIndex =  pid * numSeqsPerProcessor;
 383                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 384
 385
 386                                         //align your part
 387                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 388
 389                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 390
 391                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 392                                 }
 393
 394                                 //close files
 395                                 MPI_File_close(&inMPI);
 396                                 MPI_File_close(&outMPIAlign);
 397                                 MPI_File_close(&outMPIReport);
 398                                 MPI_File_close(&outMPIAccnos);
 399
 400                                 //delete accnos file if blank
 401                                 if (pid == 0) {
 402                                         //delete accnos file if its blank else report to user
 403                                         if (MPIWroteAccnos) {
 404                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 405                                                 if (!flip) {
 406                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 407                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 408                                                 m->mothurOutEndLine();
 409                                         }else {
 410                                                 //MPI_Info info;
 411                                                 //MPI_File_delete(outAccnosFilename, info);
 412                                                 hasAccnos = false;
 413                                                 remove(accnosFileName.c_str());
 414                                         }
 415                                 }
 416
 417 #else
 418
 419                 vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
 420                 for (int i = 0; i < (positions.size()-1); i++) {
 421                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 422                 }
 423         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 424                         if(processors == 1){
 425                                 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 426
 427                                 if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
 428
 429                                 //delete accnos file if its blank else report to user
 430                                 if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 431                                 else {
 432                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 433                                         if (!flip) {
 434                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 435                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 436                                         m->mothurOutEndLine();
 437                                 }
 438                         }else{
 439                                 processIDS.resize(0);
 440
 441                                 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 442
 443                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 444                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
 445
 446                                 //append alignment and report files
 447                                 for(int i=1;i<processors;i++){
 448                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 449                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 450
 451                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 452                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 453                                 }
 454
 455                                 vector<string> nonBlankAccnosFiles;
 456                                 //delete blank accnos files generated with multiple processes
 457                                 for(int i=0;i<processors;i++){
 458                                         if (!(m->isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 459                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 460                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 461                                 }
 462
 463                                 //append accnos files
 464                                 if (nonBlankAccnosFiles.size() != 0) {
 465                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 466
 467                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 468                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
 469                                                 remove(nonBlankAccnosFiles[h].c_str());
 470                                         }
 471                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 472                                         if (!flip) {
 473                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 474                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 475                                         m->mothurOutEndLine();
 476                                 }else{ hasAccnos = false;  }
 477
 478                                 if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
 479                         }
 480         #else
 481                         numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 482
 483                         if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear();  return 0; }
 484
 485                         //delete accnos file if its blank else report to user
 486                         if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 487                         else {
 488                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 489                                 if (!flip) {
 490                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 491                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 492                                 m->mothurOutEndLine();
 493                         }
 494
 495         #endif
 496
 497 #endif
 498
 499
 500                 #ifdef USE_MPI
 501                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 502
 503                         if (pid == 0) { //only one process should output to screen
 504                 #endif
 505
 506                         outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
 507                         outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
 508                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);  }
 509
 510                 #ifdef USE_MPI
 511                         }
 512                 #endif
 513
 514                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 515                         m->mothurOutEndLine();
 516                         m->mothurOutEndLine();
 517                 }
 518
 519
 520                 m->mothurOutEndLine();
 521                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 522                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 523                 m->mothurOutEndLine();
 524
 525                 return 0;
 526         }
 527         catch(exception& e) {
 528                 m->errorOut(e, "AlignCommand", "execute");
 529                 exit(1);
 530         }
 531 }
 532
 533 //**********************************************************************************************************************
 534
 535 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
 536         try {
 537                 ofstream alignmentFile;
 538                 m->openOutputFile(alignFName, alignmentFile);
 539
 540                 ofstream accnosFile;
 541                 m->openOutputFile(accnosFName, accnosFile);
 542
 543                 NastReport report(reportFName);
 544
 545                 ifstream inFASTA;
 546                 m->openInputFile(filename, inFASTA);
 547
 548                 inFASTA.seekg(filePos->start);
 549
 550                 bool done = false;
 551                 int count = 0;
 552
 553                 while (!done) {
 554
 555                         if (m->control_pressed) {  return 0; }
 556
 557                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 558                         report.setCandidate(candidateSeq);
 559
 560                         int origNumBases = candidateSeq->getNumBases();
 561                         string originalUnaligned = candidateSeq->getUnaligned();
 562                         int numBasesNeeded = origNumBases * threshold;
 563
 564                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 565                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 566                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 567                                 }
 568
 569                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 570                                 Sequence* templateSeq = &temp;
 571
 572                                 float searchScore = templateDB->getSearchScore();
 573
 574                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 575
 576                                 Sequence* copy;
 577
 578                                 Nast* nast2;
 579                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 580                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 581                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 582                                                                                                 //so this bool tells you if you need to delete it
 583
 584                                 //if there is a possibility that this sequence should be reversed
 585                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 586
 587                                         string wasBetter =  "";
 588                                         //if the user wants you to try the reverse
 589                                         if (flip) {
 590
 591                                                 //get reverse compliment
 592                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 593                                                 copy->reverseComplement();
 594
 595                                                 //rerun alignment
 596                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 597                                                 Sequence* templateSeq2 = &temp2;
 598
 599                                                 searchScore = templateDB->getSearchScore();
 600
 601                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 602
 603                                                 //check if any better
 604                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 605                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 606                                                         templateSeq = templateSeq2;
 607                                                         delete nast;
 608                                                         nast = nast2;
 609                                                         needToDeleteCopy = true;
 610                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 611                                                 }else{
 612                                                         wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 613                                                         delete nast2;
 614                                                         delete copy;
 615                                                 }
 616                                         }
 617
 618                                         //create accnos file with names
 619                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 620                                 }
 621
 622                                 report.setTemplate(templateSeq);
 623                                 report.setSearchParameters(search, searchScore);
 624                                 report.setAlignmentParameters(align, alignment);
 625                                 report.setNastParameters(*nast);
 626
 627                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 628
 629                                 report.print();
 630                                 delete nast;
 631                                 if (needToDeleteCopy) {   delete copy;   }
 632
 633                                 count++;
 634                         }
 635                         delete candidateSeq;
 636
 637                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 638                                 unsigned long int pos = inFASTA.tellg();
 639                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 640                         #else
 641                                 if (inFASTA.eof()) { break; }
 642                         #endif
 643
 644                         //report progress
 645                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 646
 647                 }
 648                 //report progress
 649                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 650
 651                 alignmentFile.close();
 652                 inFASTA.close();
 653                 accnosFile.close();
 654
 655                 return count;
 656         }
 657         catch(exception& e) {
 658                 m->errorOut(e, "AlignCommand", "driver");
 659                 exit(1);
 660         }
 661 }
 662 //**********************************************************************************************************************
 663 #ifdef USE_MPI
 664 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
 665         try {
 666                 string outputString = "";
 667                 MPI_Status statusReport;
 668                 MPI_Status statusAlign;
 669                 MPI_Status statusAccnos;
 670                 MPI_Status status;
 671                 int pid;
 672                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 673
 674                 NastReport report;
 675
 676                 if (pid == 0) {
 677                         outputString = report.getHeaders();
 678                         int length = outputString.length();
 679
 680                         char* buf = new char[length];
 681                         memcpy(buf, outputString.c_str(), length);
 682
 683                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 684
 685             delete buf;
 686                 }
 687
 688                 for(int i=0;i<num;i++){
 689
 690                         if (m->control_pressed) {  return 0; }
 691
 692                         //read next sequence
 693                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 694
 695                         char* buf4 = new char[length];
 696                         //memcpy(buf4, outputString.c_str(), length);
 697
 698                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 699
 700                         string tempBuf = buf4;
 701
 702                         delete buf4;
 703
 704                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 705
 706                         istringstream iss (tempBuf,istringstream::in);
 707
 708                         Sequence* candidateSeq = new Sequence(iss);
 709                         report.setCandidate(candidateSeq);
 710
 711                         int origNumBases = candidateSeq->getNumBases();
 712                         string originalUnaligned = candidateSeq->getUnaligned();
 713                         int numBasesNeeded = origNumBases * threshold;
 714
 715                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 716                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 717                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 718                                 }
 719
 720                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 721                                 Sequence* templateSeq = &temp;
 722
 723                                 float searchScore = templateDB->getSearchScore();
 724
 725                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 726                                 Sequence* copy;
 727
 728                                 Nast* nast2;
 729                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 730                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 731                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 732                                                                                                 //so this bool tells you if you need to delete it
 733
 734                                 //if there is a possibility that this sequence should be reversed
 735                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 736
 737                                         string wasBetter = "";
 738                                         //if the user wants you to try the reverse
 739                                         if (flip) {
 740                                                 //get reverse compliment
 741                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 742                                                 copy->reverseComplement();
 743
 744                                                 //rerun alignment
 745                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 746                                                 Sequence* templateSeq2 = &temp2;
 747
 748                                                 searchScore = templateDB->getSearchScore();
 749
 750                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 751
 752                                                 //check if any better
 753                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 754                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 755                                                         templateSeq = templateSeq2;
 756                                                         delete nast;
 757                                                         nast = nast2;
 758                                                         needToDeleteCopy = true;
 759                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 760                                                 }else{
 761                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 762                                                         delete nast2;
 763                                                         delete copy;
 764                                                 }
 765                                         }
 766
 767                                         //create accnos file with names
 768                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 769
 770                                         //send results to parent
 771                                         int length = outputString.length();
 772
 773                                         char* buf = new char[length];
 774                                         memcpy(buf, outputString.c_str(), length);
 775
 776                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 777                                         delete buf;
 778                                         MPIWroteAccnos = true;
 779                                 }
 780
 781                                 report.setTemplate(templateSeq);
 782                                 report.setSearchParameters(search, searchScore);
 783                                 report.setAlignmentParameters(align, alignment);
 784                                 report.setNastParameters(*nast);
 785
 786                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 787
 788                                 //send results to parent
 789                                 int length = outputString.length();
 790                                 char* buf2 = new char[length];
 791                                 memcpy(buf2, outputString.c_str(), length);
 792
 793                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 794
 795                                 delete buf2;
 796
 797                                 outputString = report.getReport();
 798
 799                                 //send results to parent
 800                                 length = outputString.length();
 801                                 char* buf3 = new char[length];
 802                                 memcpy(buf3, outputString.c_str(), length);
 803
 804                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 805
 806                                 delete buf3;
 807                                 delete nast;
 808                                 if (needToDeleteCopy) {   delete copy;   }
 809                         }
 810                         delete candidateSeq;
 811
 812                         //report progress
 813                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 814                 }
 815                 //report progress
 816                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 817
 818                 return 1;
 819         }
 820         catch(exception& e) {
 821                 m->errorOut(e, "AlignCommand", "driverMPI");
 822                 exit(1);
 823         }
 824 }
 825 #endif
 826 /**************************************************************************************************/
 827
 828 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 829         try {
 830 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 831                 int process = 0;
 832                 int num = 0;
 833                 //              processIDS.resize(0);
 834
 835                 //loop through and create all the processes you want
 836                 while (process != processors) {
 837                         int pid = fork();
 838
 839                         if (pid > 0) {
 840                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 841                                 process++;
 842                         }else if (pid == 0){
 843                                 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 844
 845                                 //pass numSeqs to parent
 846                                 ofstream out;
 847                                 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
 848                                 m->openOutputFile(tempFile, out);
 849                                 out << num << endl;
 850                                 out.close();
 851
 852                                 exit(0);
 853                         }else {
 854                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 855                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 856                                 exit(0);
 857                         }
 858                 }
 859
 860                 //force parent to wait until all the processes are done
 861                 for (int i=0;i<processors;i++) {
 862                         int temp = processIDS[i];
 863                         wait(&temp);
 864                 }
 865
 866                 for (int i = 0; i < processIDS.size(); i++) {
 867                         ifstream in;
 868                         string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
 869                         m->openInputFile(tempFile, in);
 870                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 871                         in.close(); remove(tempFile.c_str());
 872                 }
 873
 874                 return num;
 875 #endif
 876         }
 877         catch(exception& e) {
 878                 m->errorOut(e, "AlignCommand", "createProcesses");
 879                 exit(1);
 880         }
 881 }
 882 /**************************************************************************************************/
 883
 884 void AlignCommand::appendAlignFiles(string temp, string filename) {
 885         try{
 886
 887                 ofstream output;
 888                 ifstream input;
 889                 m->openOutputFileAppend(filename, output);
 890                 m->openInputFile(temp, input);
 891
 892                 while(char c = input.get()){
 893                         if(input.eof())         {       break;                  }
 894                         else                            {       output << c;    }
 895                 }
 896
 897                 input.close();
 898                 output.close();
 899         }
 900         catch(exception& e) {
 901                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 902                 exit(1);
 903         }
 904 }
 905 //**********************************************************************************************************************
 906
 907 void AlignCommand::appendReportFiles(string temp, string filename) {
 908         try{
 909
 910                 ofstream output;
 911                 ifstream input;
 912                 m->openOutputFileAppend(filename, output);
 913                 m->openInputFile(temp, input);
 914
 915                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 916
 917                 while(char c = input.get()){
 918                         if(input.eof())         {       break;                  }
 919                         else                            {       output << c;    }
 920                 }
 921
 922                 input.close();
 923                 output.close();
 924         }
 925         catch(exception& e) {
 926                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 927                 exit(1);
 928         }
 929 }
 930 //**********************************************************************************************************************