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 vector<string> AlignCommand::setParameters(){
  30         try {
  31                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  32                 CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
  33                 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
  34                 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
  35                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  36                 CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
  37                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  38                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  39                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  40                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  41                 CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
  42                 CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
  43                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  44                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  45
  46                 vector<string> myArray;
  47                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  48                 return myArray;
  49         }
  50         catch(exception& e) {
  51                 m->errorOut(e, "AlignCommand", "setParameters");
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56 string AlignCommand::getHelpString(){
  57         try {
  58                 string helpString = "";
  59                 helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.";
  60                 helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.";
  61                 helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta.";
  62                 helpString += "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.";
  63                 helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.";
  64                 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.";
  65                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
  66                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.";
  67                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.";
  68                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.";
  69                 helpString += "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.";
  70                 helpString += "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.";
  71                 helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
  72                 helpString += "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.";
  73                 helpString += "The align.seqs command should be in the following format:";
  74                 helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
  75                 helpString += "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)";
  76                 helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).";
  77                 return helpString;
  78         }
  79         catch(exception& e) {
  80                 m->errorOut(e, "AlignCommand", "getHelpString");
  81                 exit(1);
  82         }
  83 }
  84 //**********************************************************************************************************************
  85 AlignCommand::AlignCommand(){
  86         try {
  87                 abort = true; calledHelp = true;
  88                 setParameters();
  89                 vector<string> tempOutNames;
  90                 outputTypes["fasta"] = tempOutNames;
  91                 outputTypes["alignreport"] = tempOutNames;
  92                 outputTypes["accnos"] = tempOutNames;
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "AlignCommand", "AlignCommand");
  96                 exit(1);
  97         }
  98 }
  99 //**********************************************************************************************************************
 100 AlignCommand::AlignCommand(string option)  {
 101         try {
 102                 abort = false; calledHelp = false;
 103
 104                 //allow user to run help
 105                 if(option == "help") { help(); abort = true; calledHelp = true;}
 106                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 107
 108                 else {
 109                         vector<string> myArray = setParameters();
 110
 111                         OptionParser parser(option);
 112                         map<string, string> parameters = parser.getParameters();
 113
 114                         ValidParameters validParameter("align.seqs");
 115                         map<string, string>::iterator it;
 116
 117                         //check to make sure all parameters are valid for command
 118                         for (it = parameters.begin(); it != parameters.end(); it++) {
 119                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 120                         }
 121
 122                         //initialize outputTypes
 123                         vector<string> tempOutNames;
 124                         outputTypes["fasta"] = tempOutNames;
 125                         outputTypes["alignreport"] = tempOutNames;
 126                         outputTypes["accnos"] = tempOutNames;
 127
 128                         //if the user changes the output directory command factory will send this info to us in the output parameter
 129                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 130
 131
 132                         //if the user changes the input directory command factory will send this info to us in the output parameter
 133                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 134
 135                         if (inputDir == "not found"){   inputDir = "";          }
 136                         else {
 137                                 string path;
 138
 139                                 it = parameters.find("reference");
 140
 141                                 //user has given a template file
 142                                 if(it != parameters.end()){
 143                                         path = m->hasPath(it->second);
 144                                         //if the user has not given a path then, add inputdir. else leave path alone.
 145                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 146                                 }
 147                         }
 148
 149                         //check for required parameters
 150                         templateFileName = validParameter.validFile(parameters, "reference", true);
 151
 152                         if (templateFileName == "not found") {
 153                                 m->mothurOut("reference is a required parameter for the align.seqs command.");
 154                                 m->mothurOutEndLine();
 155                                 abort = true;
 156                         }else if (templateFileName == "not open") { abort = true; }
 157
 158                         candidateFileName = validParameter.validFile(parameters, "fasta", false);
 159                         if (candidateFileName == "not found") {
 160                                 //if there is a current fasta file, use it
 161                                 string filename = m->getFastaFile();
 162                                 if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 163                                 else {  m->mothurOut("You have no current fastafile and the candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
 164                         }else {
 165                                 m->splitAtDash(candidateFileName, candidateFileNames);
 166
 167                                 //go through files and make sure they are good, if not, then disregard them
 168                                 for (int i = 0; i < candidateFileNames.size(); i++) {
 169                                         //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
 170
 171                                         bool ignore = false;
 172                                         if (candidateFileNames[i] == "current") {
 173                                                 candidateFileNames[i] = m->getFastaFile();
 174                                                 if (candidateFileNames[i] != "") {  m->mothurOut("Using " + candidateFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 175                                                 else {
 176                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 177                                                         //erase from file list
 178                                                         candidateFileNames.erase(candidateFileNames.begin()+i);
 179                                                         i--;
 180                                                 }
 181                                         }
 182
 183                                         if (!ignore) {
 184
 185                                                 if (inputDir != "") {
 186                                                         string path = m->hasPath(candidateFileNames[i]);
 187                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 188                                                         if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
 189                                                 }
 190
 191                                                 int ableToOpen;
 192                                                 ifstream in;
 193                                                 ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
 194                                                 in.close();
 195
 196                                                 //if you can't open it, try default location
 197                                                 if (ableToOpen == 1) {
 198                                                         if (m->getDefaultPath() != "") { //default path is set
 199                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
 200                                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 201                                                                 ifstream in2;
 202                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 203                                                                 in2.close();
 204                                                                 candidateFileNames[i] = tryPath;
 205                                                         }
 206                                                 }
 207
 208                                                 //if you can't open it, try output location
 209                                                 if (ableToOpen == 1) {
 210                                                         if (m->getOutputDir() != "") { //default path is set
 211                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
 212                                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 213                                                                 ifstream in2;
 214                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 215                                                                 in2.close();
 216                                                                 candidateFileNames[i] = tryPath;
 217                                                         }
 218                                                 }
 219
 220
 221
 222                                                 if (ableToOpen == 1) {
 223                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 224                                                         //erase from file list
 225                                                         candidateFileNames.erase(candidateFileNames.begin()+i);
 226                                                         i--;
 227                                                 }else {
 228                                                         m->setFastaFile(candidateFileNames[i]);
 229                                                 }
 230                                         }
 231                                 }
 232
 233                                 //make sure there is at least one valid file left
 234                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 235                         }
 236
 237                         //check for optional parameter and set defaults
 238                         // ...at some point should added some additional type checking...
 239                         string temp;
 240                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 241                         convert(temp, kmerSize);
 242
 243                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 244                         convert(temp, match);
 245
 246                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 247                         convert(temp, misMatch);
 248
 249                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 250                         convert(temp, gapOpen);
 251
 252                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 253                         convert(temp, gapExtend);
 254
 255                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 256                         m->setProcessors(temp);
 257                         convert(temp, processors);
 258
 259                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 260                         flip = m->isTrue(temp);
 261
 262                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 263                         convert(temp, threshold);
 264
 265                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 266                         if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
 267
 268                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 269                         if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; }
 270
 271                 }
 272
 273         }
 274         catch(exception& e) {
 275                 m->errorOut(e, "AlignCommand", "AlignCommand");
 276                 exit(1);
 277         }
 278 }
 279 //**********************************************************************************************************************
 280 AlignCommand::~AlignCommand(){
 281
 282         if (abort == false) {
 283                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 284                 delete templateDB;
 285                 delete alignment;
 286         }
 287 }
 288 //**********************************************************************************************************************
 289
 290 int AlignCommand::execute(){
 291         try {
 292                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 293
 294                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 295                 int longestBase = templateDB->getLongestBase();
 296
 297                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 298                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 299                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 300                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 301                 else {
 302                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 303                         m->mothurOutEndLine();
 304                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 305                 }
 306
 307                 for (int s = 0; s < candidateFileNames.size(); s++) {
 308                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 309
 310                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 311
 312                         if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
 313                         string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
 314                         string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
 315                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
 316                         bool hasAccnos = true;
 317
 318                         int numFastaSeqs = 0;
 319                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 320                         int start = time(NULL);
 321
 322 #ifdef USE_MPI
 323                                 int pid, numSeqsPerProcessor;
 324                                 int tag = 2001;
 325                                 vector<unsigned long int> MPIPos;
 326                                 MPIWroteAccnos = false;
 327
 328                                 MPI_Status status;
 329                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 330                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 331
 332                                 MPI_File inMPI;
 333                                 MPI_File outMPIAlign;
 334                                 MPI_File outMPIReport;
 335                                 MPI_File outMPIAccnos;
 336
 337                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 338                                 int inMode=MPI_MODE_RDONLY;
 339
 340                                 char outAlignFilename[1024];
 341                                 strcpy(outAlignFilename, alignFileName.c_str());
 342
 343                                 char outReportFilename[1024];
 344                                 strcpy(outReportFilename, reportFileName.c_str());
 345
 346                                 char outAccnosFilename[1024];
 347                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 348
 349                                 char inFileName[1024];
 350                                 strcpy(inFileName, candidateFileNames[s].c_str());
 351
 352                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 353                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 354                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 355                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 356
 357                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 358
 359                                 if (pid == 0) { //you are the root process
 360
 361                                         MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 362
 363                                         //send file positions to all processes
 364                                         for(int i = 1; i < processors; i++) {
 365                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 366                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 367                                         }
 368
 369                                         //figure out how many sequences you have to align
 370                                         numSeqsPerProcessor = numFastaSeqs / processors;
 371                                         int startIndex =  pid * numSeqsPerProcessor;
 372                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 373
 374                                         //align your part
 375                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 376
 377                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 378
 379                                         for (int i = 1; i < processors; i++) {
 380                                                 bool tempResult;
 381                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 382                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 383                                         }
 384                                 }else{ //you are a child process
 385                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 386                                         MPIPos.resize(numFastaSeqs+1);
 387                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 388
 389
 390                                         //figure out how many sequences you have to align
 391                                         numSeqsPerProcessor = numFastaSeqs / processors;
 392                                         int startIndex =  pid * numSeqsPerProcessor;
 393                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 394
 395
 396                                         //align your part
 397                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 398
 399                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 400
 401                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 402                                 }
 403
 404                                 //close files
 405                                 MPI_File_close(&inMPI);
 406                                 MPI_File_close(&outMPIAlign);
 407                                 MPI_File_close(&outMPIReport);
 408                                 MPI_File_close(&outMPIAccnos);
 409
 410                                 //delete accnos file if blank
 411                                 if (pid == 0) {
 412                                         //delete accnos file if its blank else report to user
 413                                         if (MPIWroteAccnos) {
 414                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 415                                                 if (!flip) {
 416                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 417                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 418                                                 m->mothurOutEndLine();
 419                                         }else {
 420                                                 //MPI_Info info;
 421                                                 //MPI_File_delete(outAccnosFilename, info);
 422                                                 hasAccnos = false;
 423                                                 remove(accnosFileName.c_str());
 424                                         }
 425                                 }
 426
 427 #else
 428
 429                 vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
 430                 for (int i = 0; i < (positions.size()-1); i++) {
 431                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 432                 }
 433         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 434                         if(processors == 1){
 435                                 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 436                         }else{
 437                                 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 438                         }
 439         #else
 440                         numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 441         #endif
 442
 443                         if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear();  return 0; }
 444
 445                         //delete accnos file if its blank else report to user
 446                         if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 447                         else {
 448                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 449                                 if (!flip) {
 450                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 451                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 452                                 m->mothurOutEndLine();
 453                         }
 454
 455 #endif
 456
 457
 458                 #ifdef USE_MPI
 459                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 460
 461                         if (pid == 0) { //only one process should output to screen
 462                 #endif
 463
 464                         outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
 465                         outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
 466                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);  }
 467
 468                 #ifdef USE_MPI
 469                         }
 470                 #endif
 471
 472                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 473                         m->mothurOutEndLine();
 474                         m->mothurOutEndLine();
 475                 }
 476
 477                 //set align file as new current fastafile
 478                 string currentFasta = "";
 479                 itTypes = outputTypes.find("fasta");
 480                 if (itTypes != outputTypes.end()) {
 481                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 482                 }
 483
 484                 m->mothurOutEndLine();
 485                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 486                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 487                 m->mothurOutEndLine();
 488
 489                 return 0;
 490         }
 491         catch(exception& e) {
 492                 m->errorOut(e, "AlignCommand", "execute");
 493                 exit(1);
 494         }
 495 }
 496
 497 //**********************************************************************************************************************
 498
 499 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
 500         try {
 501                 ofstream alignmentFile;
 502                 m->openOutputFile(alignFName, alignmentFile);
 503
 504                 ofstream accnosFile;
 505                 m->openOutputFile(accnosFName, accnosFile);
 506
 507                 NastReport report(reportFName);
 508
 509                 ifstream inFASTA;
 510                 m->openInputFile(filename, inFASTA);
 511
 512                 inFASTA.seekg(filePos->start);
 513
 514                 bool done = false;
 515                 int count = 0;
 516
 517                 while (!done) {
 518
 519                         if (m->control_pressed) {  return 0; }
 520
 521                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 522                         report.setCandidate(candidateSeq);
 523
 524                         int origNumBases = candidateSeq->getNumBases();
 525                         string originalUnaligned = candidateSeq->getUnaligned();
 526                         int numBasesNeeded = origNumBases * threshold;
 527
 528                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 529                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 530                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 531                                 }
 532
 533                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 534                                 Sequence* templateSeq = &temp;
 535
 536                                 float searchScore = templateDB->getSearchScore();
 537
 538                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 539
 540                                 Sequence* copy;
 541
 542                                 Nast* nast2;
 543                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 544                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 545                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 546                                                                                                 //so this bool tells you if you need to delete it
 547
 548                                 //if there is a possibility that this sequence should be reversed
 549                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 550
 551                                         string wasBetter =  "";
 552                                         //if the user wants you to try the reverse
 553                                         if (flip) {
 554
 555                                                 //get reverse compliment
 556                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 557                                                 copy->reverseComplement();
 558
 559                                                 //rerun alignment
 560                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 561                                                 Sequence* templateSeq2 = &temp2;
 562
 563                                                 searchScore = templateDB->getSearchScore();
 564
 565                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 566
 567                                                 //check if any better
 568                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 569                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 570                                                         templateSeq = templateSeq2;
 571                                                         delete nast;
 572                                                         nast = nast2;
 573                                                         needToDeleteCopy = true;
 574                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 575                                                 }else{
 576                                                         wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 577                                                         delete nast2;
 578                                                         delete copy;
 579                                                 }
 580                                         }
 581
 582                                         //create accnos file with names
 583                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 584                                 }
 585
 586                                 report.setTemplate(templateSeq);
 587                                 report.setSearchParameters(search, searchScore);
 588                                 report.setAlignmentParameters(align, alignment);
 589                                 report.setNastParameters(*nast);
 590
 591                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 592
 593                                 report.print();
 594                                 delete nast;
 595                                 if (needToDeleteCopy) {   delete copy;   }
 596
 597                                 count++;
 598                         }
 599                         delete candidateSeq;
 600
 601                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 602                                 unsigned long int pos = inFASTA.tellg();
 603                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 604                         #else
 605                                 if (inFASTA.eof()) { break; }
 606                         #endif
 607
 608                         //report progress
 609                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 610
 611                 }
 612                 //report progress
 613                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 614
 615                 alignmentFile.close();
 616                 inFASTA.close();
 617                 accnosFile.close();
 618
 619                 return count;
 620         }
 621         catch(exception& e) {
 622                 m->errorOut(e, "AlignCommand", "driver");
 623                 exit(1);
 624         }
 625 }
 626 //**********************************************************************************************************************
 627 #ifdef USE_MPI
 628 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
 629         try {
 630                 string outputString = "";
 631                 MPI_Status statusReport;
 632                 MPI_Status statusAlign;
 633                 MPI_Status statusAccnos;
 634                 MPI_Status status;
 635                 int pid;
 636                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 637
 638                 NastReport report;
 639
 640                 if (pid == 0) {
 641                         outputString = report.getHeaders();
 642                         int length = outputString.length();
 643
 644                         char* buf = new char[length];
 645                         memcpy(buf, outputString.c_str(), length);
 646
 647                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 648
 649             delete buf;
 650                 }
 651
 652                 for(int i=0;i<num;i++){
 653
 654                         if (m->control_pressed) {  return 0; }
 655
 656                         //read next sequence
 657                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 658
 659                         char* buf4 = new char[length];
 660                         //memcpy(buf4, outputString.c_str(), length);
 661
 662                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 663
 664                         string tempBuf = buf4;
 665
 666                         delete buf4;
 667
 668                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 669
 670                         istringstream iss (tempBuf,istringstream::in);
 671
 672                         Sequence* candidateSeq = new Sequence(iss);
 673                         report.setCandidate(candidateSeq);
 674
 675                         int origNumBases = candidateSeq->getNumBases();
 676                         string originalUnaligned = candidateSeq->getUnaligned();
 677                         int numBasesNeeded = origNumBases * threshold;
 678
 679                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 680                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 681                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 682                                 }
 683
 684                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 685                                 Sequence* templateSeq = &temp;
 686
 687                                 float searchScore = templateDB->getSearchScore();
 688
 689                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 690                                 Sequence* copy;
 691
 692                                 Nast* nast2;
 693                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 694                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 695                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 696                                                                                                 //so this bool tells you if you need to delete it
 697
 698                                 //if there is a possibility that this sequence should be reversed
 699                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 700
 701                                         string wasBetter = "";
 702                                         //if the user wants you to try the reverse
 703                                         if (flip) {
 704                                                 //get reverse compliment
 705                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 706                                                 copy->reverseComplement();
 707
 708                                                 //rerun alignment
 709                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 710                                                 Sequence* templateSeq2 = &temp2;
 711
 712                                                 searchScore = templateDB->getSearchScore();
 713
 714                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 715
 716                                                 //check if any better
 717                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 718                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 719                                                         templateSeq = templateSeq2;
 720                                                         delete nast;
 721                                                         nast = nast2;
 722                                                         needToDeleteCopy = true;
 723                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 724                                                 }else{
 725                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 726                                                         delete nast2;
 727                                                         delete copy;
 728                                                 }
 729                                         }
 730
 731                                         //create accnos file with names
 732                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 733
 734                                         //send results to parent
 735                                         int length = outputString.length();
 736
 737                                         char* buf = new char[length];
 738                                         memcpy(buf, outputString.c_str(), length);
 739
 740                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 741                                         delete buf;
 742                                         MPIWroteAccnos = true;
 743                                 }
 744
 745                                 report.setTemplate(templateSeq);
 746                                 report.setSearchParameters(search, searchScore);
 747                                 report.setAlignmentParameters(align, alignment);
 748                                 report.setNastParameters(*nast);
 749
 750                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 751
 752                                 //send results to parent
 753                                 int length = outputString.length();
 754                                 char* buf2 = new char[length];
 755                                 memcpy(buf2, outputString.c_str(), length);
 756
 757                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 758
 759                                 delete buf2;
 760
 761                                 outputString = report.getReport();
 762
 763                                 //send results to parent
 764                                 length = outputString.length();
 765                                 char* buf3 = new char[length];
 766                                 memcpy(buf3, outputString.c_str(), length);
 767
 768                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 769
 770                                 delete buf3;
 771                                 delete nast;
 772                                 if (needToDeleteCopy) {   delete copy;   }
 773                         }
 774                         delete candidateSeq;
 775
 776                         //report progress
 777                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 778                 }
 779                 //report progress
 780                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 781
 782                 return 1;
 783         }
 784         catch(exception& e) {
 785                 m->errorOut(e, "AlignCommand", "driverMPI");
 786                 exit(1);
 787         }
 788 }
 789 #endif
 790 /**************************************************************************************************/
 791
 792 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 793         try {
 794 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 795                 processIDS.resize(0);
 796                 int process = 1;
 797                 int num = 0;
 798                 //              processIDS.resize(0);
 799
 800                 //loop through and create all the processes you want
 801                 while (process != processors) {
 802                         int pid = fork();
 803
 804                         if (pid > 0) {
 805                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 806                                 process++;
 807                         }else if (pid == 0){
 808                                 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 809
 810                                 //pass numSeqs to parent
 811                                 ofstream out;
 812                                 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
 813                                 m->openOutputFile(tempFile, out);
 814                                 out << num << endl;
 815                                 out.close();
 816
 817                                 exit(0);
 818                         }else {
 819                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 820                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 821                                 exit(0);
 822                         }
 823                 }
 824
 825                 //do my part
 826                 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
 827
 828                 //force parent to wait until all the processes are done
 829                 for (int i=0;i<processIDS.size();i++) {
 830                         int temp = processIDS[i];
 831                         wait(&temp);
 832                 }
 833
 834                 vector<string> nonBlankAccnosFiles;
 835                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 836                 else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it
 837
 838                 for (int i = 0; i < processIDS.size(); i++) {
 839                         ifstream in;
 840                         string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
 841                         m->openInputFile(tempFile, in);
 842                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 843                         in.close(); remove(tempFile.c_str());
 844
 845                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 846                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 847
 848                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 849                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 850
 851                         if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
 852                                 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
 853                         }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str());  }
 854
 855                 }
 856
 857                 //append accnos files
 858                 if (nonBlankAccnosFiles.size() != 0) {
 859                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 860
 861                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 862                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
 863                                 remove(nonBlankAccnosFiles[h].c_str());
 864                         }
 865                 }else { //recreate the accnosfile if needed
 866                         ofstream out;
 867                         m->openOutputFile(accnosFName, out);
 868                         out.close();
 869                 }
 870
 871                 return num;
 872 #endif
 873         }
 874         catch(exception& e) {
 875                 m->errorOut(e, "AlignCommand", "createProcesses");
 876                 exit(1);
 877         }
 878 }
 879 /**************************************************************************************************/
 880
 881 void AlignCommand::appendAlignFiles(string temp, string filename) {
 882         try{
 883
 884                 ofstream output;
 885                 ifstream input;
 886                 m->openOutputFileAppend(filename, output);
 887                 m->openInputFile(temp, input);
 888
 889                 while(char c = input.get()){
 890                         if(input.eof())         {       break;                  }
 891                         else                            {       output << c;    }
 892                 }
 893
 894                 input.close();
 895                 output.close();
 896         }
 897         catch(exception& e) {
 898                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 899                 exit(1);
 900         }
 901 }
 902 //**********************************************************************************************************************
 903
 904 void AlignCommand::appendReportFiles(string temp, string filename) {
 905         try{
 906
 907                 ofstream output;
 908                 ifstream input;
 909                 m->openOutputFileAppend(filename, output);
 910                 m->openInputFile(temp, input);
 911
 912                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 913
 914                 while(char c = input.get()){
 915                         if(input.eof())         {       break;                  }
 916                         else                            {       output << c;    }
 917                 }
 918
 919                 input.close();
 920                 output.close();
 921         }
 922         catch(exception& e) {
 923                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 924                 exit(1);
 925         }
 926 }
 927 //**********************************************************************************************************************