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 #include "referencedb.h"
  28
  29 //**********************************************************************************************************************
  30 vector<string> AlignCommand::setParameters(){
  31         try {
  32                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  33                 CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
  34                 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
  35                 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
  36                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  37                 CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
  38                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  39                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  40                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  41                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  42                 CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
  43                 CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
  44                 CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
  45                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  46                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  47
  48                 vector<string> myArray;
  49                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  50                 return myArray;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "AlignCommand", "setParameters");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 string AlignCommand::getHelpString(){
  59         try {
  60                 string helpString = "";
  61                 helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.";
  62                 helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.";
  63                 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.";
  64                 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.";
  65                 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.";
  66                 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.";
  67                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
  68                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.";
  69                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.";
  70                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.";
  71                 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.";
  72                 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.";
  73                 helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
  74                 helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
  75                 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.";
  76                 helpString += "The align.seqs command should be in the following format:";
  77                 helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
  78                 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)";
  79                 helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).";
  80                 return helpString;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "AlignCommand", "getHelpString");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88 AlignCommand::AlignCommand(){
  89         try {
  90                 abort = true; calledHelp = true;
  91                 setParameters();
  92                 vector<string> tempOutNames;
  93                 outputTypes["fasta"] = tempOutNames;
  94                 outputTypes["alignreport"] = tempOutNames;
  95                 outputTypes["accnos"] = tempOutNames;
  96         }
  97         catch(exception& e) {
  98                 m->errorOut(e, "AlignCommand", "AlignCommand");
  99                 exit(1);
 100         }
 101 }
 102 //**********************************************************************************************************************
 103 AlignCommand::AlignCommand(string option)  {
 104         try {
 105                 abort = false; calledHelp = false;
 106                 ReferenceDB* rdb = ReferenceDB::getInstance();
 107
 108                 //allow user to run help
 109                 if(option == "help") { help(); abort = true; calledHelp = true;}
 110                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 111
 112                 else {
 113                         vector<string> myArray = setParameters();
 114
 115                         OptionParser parser(option);
 116                         map<string, string> parameters = parser.getParameters();
 117
 118                         ValidParameters validParameter("align.seqs");
 119                         map<string, string>::iterator it;
 120
 121                         //check to make sure all parameters are valid for command
 122                         for (it = parameters.begin(); it != parameters.end(); it++) {
 123                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 124                         }
 125
 126                         //initialize outputTypes
 127                         vector<string> tempOutNames;
 128                         outputTypes["fasta"] = tempOutNames;
 129                         outputTypes["alignreport"] = tempOutNames;
 130                         outputTypes["accnos"] = tempOutNames;
 131
 132                         //if the user changes the output directory command factory will send this info to us in the output parameter
 133                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 134
 135
 136                         //if the user changes the input directory command factory will send this info to us in the output parameter
 137                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 138
 139                         if (inputDir == "not found"){   inputDir = "";          }
 140                         else {
 141                                 string path;
 142
 143                                 it = parameters.find("reference");
 144
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 150                                 }
 151                         }
 152
 153                         candidateFileName = validParameter.validFile(parameters, "fasta", false);
 154                         if (candidateFileName == "not found") {
 155                                 //if there is a current fasta file, use it
 156                                 string filename = m->getFastaFile();
 157                                 if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 158                                 else {  m->mothurOut("You have no current fastafile and the candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
 159                         }else {
 160                                 m->splitAtDash(candidateFileName, candidateFileNames);
 161
 162                                 //go through files and make sure they are good, if not, then disregard them
 163                                 for (int i = 0; i < candidateFileNames.size(); i++) {
 164                                         //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
 165
 166                                         bool ignore = false;
 167                                         if (candidateFileNames[i] == "current") {
 168                                                 candidateFileNames[i] = m->getFastaFile();
 169                                                 if (candidateFileNames[i] != "") {  m->mothurOut("Using " + candidateFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 170                                                 else {
 171                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 172                                                         //erase from file list
 173                                                         candidateFileNames.erase(candidateFileNames.begin()+i);
 174                                                         i--;
 175                                                 }
 176                                         }
 177
 178                                         if (!ignore) {
 179
 180                                                 if (inputDir != "") {
 181                                                         string path = m->hasPath(candidateFileNames[i]);
 182                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 183                                                         if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
 184                                                 }
 185
 186                                                 int ableToOpen;
 187                                                 ifstream in;
 188                                                 ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
 189                                                 in.close();
 190
 191                                                 //if you can't open it, try default location
 192                                                 if (ableToOpen == 1) {
 193                                                         if (m->getDefaultPath() != "") { //default path is set
 194                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
 195                                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 196                                                                 ifstream in2;
 197                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 198                                                                 in2.close();
 199                                                                 candidateFileNames[i] = tryPath;
 200                                                         }
 201                                                 }
 202
 203                                                 //if you can't open it, try output location
 204                                                 if (ableToOpen == 1) {
 205                                                         if (m->getOutputDir() != "") { //default path is set
 206                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
 207                                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 208                                                                 ifstream in2;
 209                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 210                                                                 in2.close();
 211                                                                 candidateFileNames[i] = tryPath;
 212                                                         }
 213                                                 }
 214
 215
 216
 217                                                 if (ableToOpen == 1) {
 218                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 219                                                         //erase from file list
 220                                                         candidateFileNames.erase(candidateFileNames.begin()+i);
 221                                                         i--;
 222                                                 }else {
 223                                                         m->setFastaFile(candidateFileNames[i]);
 224                                                 }
 225                                         }
 226                                 }
 227
 228                                 //make sure there is at least one valid file left
 229                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 230                         }
 231
 232                         //check for optional parameter and set defaults
 233                         // ...at some point should added some additional type checking...
 234                         string temp;
 235                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 236                         convert(temp, kmerSize);
 237
 238                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 239                         convert(temp, match);
 240
 241                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 242                         convert(temp, misMatch);
 243
 244                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 245                         convert(temp, gapOpen);
 246
 247                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 248                         convert(temp, gapExtend);
 249
 250                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 251                         m->setProcessors(temp);
 252                         convert(temp, processors);
 253
 254                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 255                         flip = m->isTrue(temp);
 256
 257                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 258                         save = m->isTrue(temp);
 259                         rdb->save = save;
 260                         if (save) { //clear out old references
 261                                 rdb->clearMemory();
 262                         }
 263
 264                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 265                         templateFileName = validParameter.validFile(parameters, "reference", true);
 266                         if (templateFileName == "not found") {
 267                                 //check for saved reference sequences
 268                                 if (rdb->referenceSeqs.size() != 0) {
 269                                         templateFileName = "saved";
 270                                 }else {
 271                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the align.seqs command.");
 272                                         m->mothurOutEndLine();
 273                                         abort = true;
 274                                 }
 275                         }else if (templateFileName == "not open") { abort = true; }
 276                         else {  if (save) {     rdb->setSavedReference(templateFileName);       }       }
 277
 278                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 279                         convert(temp, threshold);
 280
 281                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 282                         if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
 283
 284                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 285                         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; }
 286
 287                 }
 288
 289         }
 290         catch(exception& e) {
 291                 m->errorOut(e, "AlignCommand", "AlignCommand");
 292                 exit(1);
 293         }
 294 }
 295 //**********************************************************************************************************************
 296 AlignCommand::~AlignCommand(){
 297
 298         if (abort == false) {
 299                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 300                 delete templateDB;
 301                 delete alignment;
 302         }
 303 }
 304 //**********************************************************************************************************************
 305
 306 int AlignCommand::execute(){
 307         try {
 308                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 309
 310                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 311                 int longestBase = templateDB->getLongestBase();
 312
 313                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 314                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 315                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 316                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 317                 else {
 318                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 319                         m->mothurOutEndLine();
 320                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 321                 }
 322
 323                 for (int s = 0; s < candidateFileNames.size(); s++) {
 324                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 325
 326                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 327
 328                         if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
 329                         string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
 330                         string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
 331                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
 332                         bool hasAccnos = true;
 333
 334                         int numFastaSeqs = 0;
 335                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 336                         int start = time(NULL);
 337
 338 #ifdef USE_MPI
 339                                 int pid, numSeqsPerProcessor;
 340                                 int tag = 2001;
 341                                 vector<unsigned long int> MPIPos;
 342                                 MPIWroteAccnos = false;
 343
 344                                 MPI_Status status;
 345                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 346                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 347
 348                                 MPI_File inMPI;
 349                                 MPI_File outMPIAlign;
 350                                 MPI_File outMPIReport;
 351                                 MPI_File outMPIAccnos;
 352
 353                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 354                                 int inMode=MPI_MODE_RDONLY;
 355
 356                                 char outAlignFilename[1024];
 357                                 strcpy(outAlignFilename, alignFileName.c_str());
 358
 359                                 char outReportFilename[1024];
 360                                 strcpy(outReportFilename, reportFileName.c_str());
 361
 362                                 char outAccnosFilename[1024];
 363                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 364
 365                                 char inFileName[1024];
 366                                 strcpy(inFileName, candidateFileNames[s].c_str());
 367
 368                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 369                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 370                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 371                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 372
 373                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 374
 375                                 if (pid == 0) { //you are the root process
 376
 377                                         MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 378
 379                                         //send file positions to all processes
 380                                         for(int i = 1; i < processors; i++) {
 381                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 382                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 383                                         }
 384
 385                                         //figure out how many sequences you have to align
 386                                         numSeqsPerProcessor = numFastaSeqs / processors;
 387                                         int startIndex =  pid * numSeqsPerProcessor;
 388                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 389
 390                                         //align your part
 391                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 392
 393                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 394
 395                                         for (int i = 1; i < processors; i++) {
 396                                                 bool tempResult;
 397                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 398                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 399                                         }
 400                                 }else{ //you are a child process
 401                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 402                                         MPIPos.resize(numFastaSeqs+1);
 403                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 404
 405
 406                                         //figure out how many sequences you have to align
 407                                         numSeqsPerProcessor = numFastaSeqs / processors;
 408                                         int startIndex =  pid * numSeqsPerProcessor;
 409                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 410
 411
 412                                         //align your part
 413                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 414
 415                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 416
 417                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 418                                 }
 419
 420                                 //close files
 421                                 MPI_File_close(&inMPI);
 422                                 MPI_File_close(&outMPIAlign);
 423                                 MPI_File_close(&outMPIReport);
 424                                 MPI_File_close(&outMPIAccnos);
 425
 426                                 //delete accnos file if blank
 427                                 if (pid == 0) {
 428                                         //delete accnos file if its blank else report to user
 429                                         if (MPIWroteAccnos) {
 430                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 431                                                 if (!flip) {
 432                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 433                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 434                                                 m->mothurOutEndLine();
 435                                         }else {
 436                                                 //MPI_Info info;
 437                                                 //MPI_File_delete(outAccnosFilename, info);
 438                                                 hasAccnos = false;
 439                                                 m->mothurRemove(accnosFileName);
 440                                         }
 441                                 }
 442
 443 #else
 444
 445                 vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
 446                 for (int i = 0; i < (positions.size()-1); i++) {
 447                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 448                 }
 449         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 450                         if(processors == 1){
 451                                 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 452                         }else{
 453                                 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 454                         }
 455         #else
 456                         numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 457         #endif
 458
 459                         if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(alignFileName); m->mothurRemove(reportFileName); outputTypes.clear();  return 0; }
 460
 461                         //delete accnos file if its blank else report to user
 462                         if (m->isBlank(accnosFileName)) {  m->mothurRemove(accnosFileName);  hasAccnos = false; }
 463                         else {
 464                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 465                                 if (!flip) {
 466                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 467                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 468                                 m->mothurOutEndLine();
 469                         }
 470
 471 #endif
 472
 473
 474                 #ifdef USE_MPI
 475                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 476
 477                         if (pid == 0) { //only one process should output to screen
 478                 #endif
 479
 480                         outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
 481                         outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
 482                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);  }
 483
 484                 #ifdef USE_MPI
 485                         }
 486                 #endif
 487
 488                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 489                         m->mothurOutEndLine();
 490                         m->mothurOutEndLine();
 491                 }
 492
 493                 //set align file as new current fastafile
 494                 string currentFasta = "";
 495                 itTypes = outputTypes.find("fasta");
 496                 if (itTypes != outputTypes.end()) {
 497                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 498                 }
 499
 500                 m->mothurOutEndLine();
 501                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 502                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 503                 m->mothurOutEndLine();
 504
 505                 return 0;
 506         }
 507         catch(exception& e) {
 508                 m->errorOut(e, "AlignCommand", "execute");
 509                 exit(1);
 510         }
 511 }
 512
 513 //**********************************************************************************************************************
 514
 515 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
 516         try {
 517                 ofstream alignmentFile;
 518                 m->openOutputFile(alignFName, alignmentFile);
 519
 520                 ofstream accnosFile;
 521                 m->openOutputFile(accnosFName, accnosFile);
 522
 523                 NastReport report(reportFName);
 524
 525                 ifstream inFASTA;
 526                 m->openInputFile(filename, inFASTA);
 527
 528                 inFASTA.seekg(filePos->start);
 529
 530                 bool done = false;
 531                 int count = 0;
 532
 533                 while (!done) {
 534
 535                         if (m->control_pressed) {  return 0; }
 536
 537                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 538                         report.setCandidate(candidateSeq);
 539
 540                         int origNumBases = candidateSeq->getNumBases();
 541                         string originalUnaligned = candidateSeq->getUnaligned();
 542                         int numBasesNeeded = origNumBases * threshold;
 543
 544                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 545                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 546                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 547                                 }
 548
 549                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 550                                 Sequence* templateSeq = &temp;
 551
 552                                 float searchScore = templateDB->getSearchScore();
 553
 554                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 555
 556                                 Sequence* copy;
 557
 558                                 Nast* nast2;
 559                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 560                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 561                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 562                                                                                                 //so this bool tells you if you need to delete it
 563
 564                                 //if there is a possibility that this sequence should be reversed
 565                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 566
 567                                         string wasBetter =  "";
 568                                         //if the user wants you to try the reverse
 569                                         if (flip) {
 570
 571                                                 //get reverse compliment
 572                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 573                                                 copy->reverseComplement();
 574
 575                                                 //rerun alignment
 576                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 577                                                 Sequence* templateSeq2 = &temp2;
 578
 579                                                 searchScore = templateDB->getSearchScore();
 580
 581                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 582
 583                                                 //check if any better
 584                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 585                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 586                                                         templateSeq = templateSeq2;
 587                                                         delete nast;
 588                                                         nast = nast2;
 589                                                         needToDeleteCopy = true;
 590                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 591                                                 }else{
 592                                                         wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 593                                                         delete nast2;
 594                                                         delete copy;
 595                                                 }
 596                                         }
 597
 598                                         //create accnos file with names
 599                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 600                                 }
 601
 602                                 report.setTemplate(templateSeq);
 603                                 report.setSearchParameters(search, searchScore);
 604                                 report.setAlignmentParameters(align, alignment);
 605                                 report.setNastParameters(*nast);
 606
 607                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 608
 609                                 report.print();
 610                                 delete nast;
 611                                 if (needToDeleteCopy) {   delete copy;   }
 612
 613                                 count++;
 614                         }
 615                         delete candidateSeq;
 616
 617                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 618                                 unsigned long int pos = inFASTA.tellg();
 619                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 620                         #else
 621                                 if (inFASTA.eof()) { break; }
 622                         #endif
 623
 624                         //report progress
 625                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 626
 627                 }
 628                 //report progress
 629                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 630
 631                 alignmentFile.close();
 632                 inFASTA.close();
 633                 accnosFile.close();
 634
 635                 return count;
 636         }
 637         catch(exception& e) {
 638                 m->errorOut(e, "AlignCommand", "driver");
 639                 exit(1);
 640         }
 641 }
 642 //**********************************************************************************************************************
 643 #ifdef USE_MPI
 644 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
 645         try {
 646                 string outputString = "";
 647                 MPI_Status statusReport;
 648                 MPI_Status statusAlign;
 649                 MPI_Status statusAccnos;
 650                 MPI_Status status;
 651                 int pid;
 652                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 653
 654                 NastReport report;
 655
 656                 if (pid == 0) {
 657                         outputString = report.getHeaders();
 658                         int length = outputString.length();
 659
 660                         char* buf = new char[length];
 661                         memcpy(buf, outputString.c_str(), length);
 662
 663                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 664
 665             delete buf;
 666                 }
 667
 668                 for(int i=0;i<num;i++){
 669
 670                         if (m->control_pressed) {  return 0; }
 671
 672                         //read next sequence
 673                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 674
 675                         char* buf4 = new char[length];
 676                         //memcpy(buf4, outputString.c_str(), length);
 677
 678                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 679
 680                         string tempBuf = buf4;
 681
 682                         delete buf4;
 683
 684                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 685
 686                         istringstream iss (tempBuf,istringstream::in);
 687
 688                         Sequence* candidateSeq = new Sequence(iss);
 689                         report.setCandidate(candidateSeq);
 690
 691                         int origNumBases = candidateSeq->getNumBases();
 692                         string originalUnaligned = candidateSeq->getUnaligned();
 693                         int numBasesNeeded = origNumBases * threshold;
 694
 695                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 696                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 697                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 698                                 }
 699
 700                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 701                                 Sequence* templateSeq = &temp;
 702
 703                                 float searchScore = templateDB->getSearchScore();
 704
 705                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 706                                 Sequence* copy;
 707
 708                                 Nast* nast2;
 709                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 710                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 711                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 712                                                                                                 //so this bool tells you if you need to delete it
 713
 714                                 //if there is a possibility that this sequence should be reversed
 715                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 716
 717                                         string wasBetter = "";
 718                                         //if the user wants you to try the reverse
 719                                         if (flip) {
 720                                                 //get reverse compliment
 721                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 722                                                 copy->reverseComplement();
 723
 724                                                 //rerun alignment
 725                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 726                                                 Sequence* templateSeq2 = &temp2;
 727
 728                                                 searchScore = templateDB->getSearchScore();
 729
 730                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 731
 732                                                 //check if any better
 733                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 734                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 735                                                         templateSeq = templateSeq2;
 736                                                         delete nast;
 737                                                         nast = nast2;
 738                                                         needToDeleteCopy = true;
 739                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 740                                                 }else{
 741                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 742                                                         delete nast2;
 743                                                         delete copy;
 744                                                 }
 745                                         }
 746
 747                                         //create accnos file with names
 748                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 749
 750                                         //send results to parent
 751                                         int length = outputString.length();
 752
 753                                         char* buf = new char[length];
 754                                         memcpy(buf, outputString.c_str(), length);
 755
 756                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 757                                         delete buf;
 758                                         MPIWroteAccnos = true;
 759                                 }
 760
 761                                 report.setTemplate(templateSeq);
 762                                 report.setSearchParameters(search, searchScore);
 763                                 report.setAlignmentParameters(align, alignment);
 764                                 report.setNastParameters(*nast);
 765
 766                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 767
 768                                 //send results to parent
 769                                 int length = outputString.length();
 770                                 char* buf2 = new char[length];
 771                                 memcpy(buf2, outputString.c_str(), length);
 772
 773                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 774
 775                                 delete buf2;
 776
 777                                 outputString = report.getReport();
 778
 779                                 //send results to parent
 780                                 length = outputString.length();
 781                                 char* buf3 = new char[length];
 782                                 memcpy(buf3, outputString.c_str(), length);
 783
 784                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 785
 786                                 delete buf3;
 787                                 delete nast;
 788                                 if (needToDeleteCopy) {   delete copy;   }
 789                         }
 790                         delete candidateSeq;
 791
 792                         //report progress
 793                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 794                 }
 795                 //report progress
 796                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 797
 798                 return 1;
 799         }
 800         catch(exception& e) {
 801                 m->errorOut(e, "AlignCommand", "driverMPI");
 802                 exit(1);
 803         }
 804 }
 805 #endif
 806 /**************************************************************************************************/
 807
 808 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 809         try {
 810 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 811                 processIDS.resize(0);
 812                 int process = 1;
 813                 int num = 0;
 814                 //              processIDS.resize(0);
 815
 816                 //loop through and create all the processes you want
 817                 while (process != processors) {
 818                         int pid = fork();
 819
 820                         if (pid > 0) {
 821                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 822                                 process++;
 823                         }else if (pid == 0){
 824                                 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 825
 826                                 //pass numSeqs to parent
 827                                 ofstream out;
 828                                 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
 829                                 m->openOutputFile(tempFile, out);
 830                                 out << num << endl;
 831                                 out.close();
 832
 833                                 exit(0);
 834                         }else {
 835                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 836                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 837                                 exit(0);
 838                         }
 839                 }
 840
 841                 //do my part
 842                 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
 843
 844                 //force parent to wait until all the processes are done
 845                 for (int i=0;i<processIDS.size();i++) {
 846                         int temp = processIDS[i];
 847                         wait(&temp);
 848                 }
 849
 850                 vector<string> nonBlankAccnosFiles;
 851                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 852                 else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
 853
 854                 for (int i = 0; i < processIDS.size(); i++) {
 855                         ifstream in;
 856                         string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
 857                         m->openInputFile(tempFile, in);
 858                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 859                         in.close(); m->mothurRemove(tempFile);
 860
 861                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 862                         m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
 863
 864                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 865                         m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
 866
 867                         if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
 868                                 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
 869                         }else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp"));  }
 870
 871                 }
 872
 873                 //append accnos files
 874                 if (nonBlankAccnosFiles.size() != 0) {
 875                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 876
 877                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 878                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
 879                                 m->mothurRemove(nonBlankAccnosFiles[h]);
 880                         }
 881                 }else { //recreate the accnosfile if needed
 882                         ofstream out;
 883                         m->openOutputFile(accnosFName, out);
 884                         out.close();
 885                 }
 886
 887                 return num;
 888 #endif
 889         }
 890         catch(exception& e) {
 891                 m->errorOut(e, "AlignCommand", "createProcesses");
 892                 exit(1);
 893         }
 894 }
 895 /**************************************************************************************************/
 896
 897 void AlignCommand::appendAlignFiles(string temp, string filename) {
 898         try{
 899
 900                 ofstream output;
 901                 ifstream input;
 902                 m->openOutputFileAppend(filename, output);
 903                 m->openInputFile(temp, input);
 904
 905                 while(char c = input.get()){
 906                         if(input.eof())         {       break;                  }
 907                         else                            {       output << c;    }
 908                 }
 909
 910                 input.close();
 911                 output.close();
 912         }
 913         catch(exception& e) {
 914                 m->errorOut(e, "AlignCommand", "appendAlignFiles");
 915                 exit(1);
 916         }
 917 }
 918 //**********************************************************************************************************************
 919
 920 void AlignCommand::appendReportFiles(string temp, string filename) {
 921         try{
 922
 923                 ofstream output;
 924                 ifstream input;
 925                 m->openOutputFileAppend(filename, output);
 926                 m->openInputFile(temp, input);
 927
 928                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 929
 930                 while(char c = input.get()){
 931                         if(input.eof())         {       break;                  }
 932                         else                            {       output << c;    }
 933                 }
 934
 935                 input.close();
 936                 output.close();
 937         }
 938         catch(exception& e) {
 939                 m->errorOut(e, "AlignCommand", "appendReportFiles");
 940                 exit(1);
 941         }
 942 }
 943 //**********************************************************************************************************************