aligncommand.cpp

   1 /*\r
   2  *  aligncommand.cpp\r
   3  *  Mothur\r
   4  *\r
   5  *  Created by Sarah Westcott on 5/15/09.\r
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.\r
   7  *\r
   8  *      This version of nast does everything I think that the greengenes nast server does and then some.  I have added the \r
   9  *      feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment \r
  10  *      method.  This latter feature is perhaps most significant.  nastPlus enables a user to use either a Needleman-Wunsch \r
  11  *      (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm.  This is significant because it\r
  12  *      allows for a global alignment and not the local alignment provided by bLAst.  Furthermore, it has the potential to\r
  13  *      provide a better alignment because of the banding method employed by blast (I'm not sure about this).\r
  14  *\r
  15  */\r
  16 \r
  17 #include "aligncommand.h"\r
  18 #include "sequence.hpp"\r
  19 \r
  20 #include "gotohoverlap.hpp"\r
  21 #include "needlemanoverlap.hpp"\r
  22 #include "blastalign.hpp"\r
  23 #include "noalign.hpp"\r
  24 \r
  25 #include "nast.hpp"\r
  26 #include "nastreport.hpp"\r
  27 \r
  28 \r
  29 //**********************************************************************************************************************\r
  30 \r
  31 AlignCommand::AlignCommand(string option)  {\r
  32         try {\r
  33                 \r
  34                 abort = false;\r
  35         \r
  36                 //allow user to run help\r
  37                 if(option == "help") { help(); abort = true; }\r
  38                 \r
  39                 else {\r
  40                         \r
  41                         //valid paramters for this command\r
  42                         string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};\r
  43                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));\r
  44                         \r
  45                         OptionParser parser(option);\r
  46                         map<string, string> parameters = parser.getParameters(); \r
  47                         \r
  48                         ValidParameters validParameter;\r
  49                         map<string, string>::iterator it;\r
  50                         \r
  51                         //check to make sure all parameters are valid for command\r
  52                         for (it = parameters.begin(); it != parameters.end(); it++) { \r
  53                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }\r
  54                         }\r
  55 \r
  56                         //if the user changes the output directory command factory will send this info to us in the output parameter \r
  57                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }\r
  58                         \r
  59 \r
  60                         //if the user changes the input directory command factory will send this info to us in the output parameter \r
  61                         string inputDir = validParameter.validFile(parameters, "inputdir", false);              \r
  62                         \r
  63                         if (inputDir == "not found"){   inputDir = "";          }\r
  64                         else {\r
  65                                 string path;\r
  66 \r
  67                                 it = parameters.find("template");\r
  68 \r
  69                                 //user has given a template file\r
  70                                 if(it != parameters.end()){ \r
  71                                         path = hasPath(it->second);\r
  72                                         //if the user has not given a path then, add inputdir. else leave path alone.\r
  73                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }\r
  74                                 }\r
  75                         }\r
  76 \r
  77                         //check for required parameters\r
  78                         templateFileName = validParameter.validFile(parameters, "template", true);\r
  79                         \r
  80                         if (templateFileName == "not found") { \r
  81                                 m->mothurOut("template is a required parameter for the align.seqs command."); \r
  82                                 m->mothurOutEndLine();\r
  83                                 abort = true; \r
  84                         }else if (templateFileName == "not open") { abort = true; }     \r
  85                         \r
  86                         candidateFileName = validParameter.validFile(parameters, "candidate", false);\r
  87                         if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true;  }\r
  88                         else { \r
  89                                 splitAtDash(candidateFileName, candidateFileNames);\r
  90                                 \r
  91                                 //go through files and make sure they are good, if not, then disregard them\r
  92                                 for (int i = 0; i < candidateFileNames.size(); i++) {\r
  93                                         if (inputDir != "") {\r
  94                                                 string path = hasPath(candidateFileNames[i]);\r
  95                                                 //if the user has not given a path then, add inputdir. else leave path alone.\r
  96                                                 if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }\r
  97                                         }\r
  98         \r
  99                                         int ableToOpen;\r
 100                                         ifstream in;\r
 101                                         \r
 102                                         #ifdef USE_MPI  \r
 103                                                 int pid;\r
 104                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running\r
 105                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are\r
 106                                 \r
 107                                                 if (pid == 0) {\r
 108                                         #endif\r
 109 \r
 110                                         ableToOpen = openInputFile(candidateFileNames[i], in);\r
 111                                         in.close();\r
 112                                         \r
 113                                         #ifdef USE_MPI  \r
 114                                                         for (int j = 1; j < processors; j++) {\r
 115                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); \r
 116                                                         }\r
 117                                                 }else{\r
 118                                                         MPI_Status status;\r
 119                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);\r
 120                                                 }\r
 121                                                 \r
 122                                         #endif\r
 123 \r
 124                                         if (ableToOpen == 1) { \r
 125                                                 m->mothurOut(candidateFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); \r
 126                                                 //erase from file list\r
 127                                                 candidateFileNames.erase(candidateFileNames.begin()+i);\r
 128                                                 i--;\r
 129                                         }\r
 130                                         \r
 131                                 }\r
 132                                 \r
 133                                 //make sure there is at least one valid file left\r
 134                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }\r
 135                         }\r
 136                 \r
 137                         //check for optional parameter and set defaults\r
 138                         // ...at some point should added some additional type checking...\r
 139                         string temp;\r
 140                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }\r
 141                         convert(temp, kmerSize); \r
 142                         \r
 143                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }\r
 144                         convert(temp, match);  \r
 145                         \r
 146                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }\r
 147                         convert(temp, misMatch);  \r
 148                         \r
 149                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }\r
 150                         convert(temp, gapOpen);  \r
 151                         \r
 152                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }\r
 153                         convert(temp, gapExtend); \r
 154                         \r
 155                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }\r
 156                         convert(temp, processors); \r
 157                         \r
 158                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }\r
 159                         flip = isTrue(temp); \r
 160                         \r
 161                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }\r
 162                         convert(temp, threshold); \r
 163                         \r
 164                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }\r
 165                         \r
 166                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }\r
 167                 }\r
 168                 \r
 169         }\r
 170         catch(exception& e) {\r
 171                 m->errorOut(e, "AlignCommand", "AlignCommand");\r
 172                 exit(1);\r
 173         }\r
 174 }\r
 175 \r
 176 //**********************************************************************************************************************\r
 177 \r
 178 AlignCommand::~AlignCommand(){  \r
 179 \r
 180         if (abort == false) {\r
 181                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();\r
 182                 delete templateDB;\r
 183                 delete alignment;\r
 184         }\r
 185 }\r
 186 \r
 187 //**********************************************************************************************************************\r
 188 \r
 189 void AlignCommand::help(){\r
 190         try {\r
 191                 m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");\r
 192                 m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");\r
 193                 m->mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");\r
 194                 m->mothurOut("The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer.\n");\r
 195                 m->mothurOut("The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");\r
 196                 m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");\r
 197                 m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");\r
 198                 m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");\r
 199                 m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");\r
 200                 m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");\r
 201                 m->mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold.  The default is false.\n");\r
 202                 m->mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n");\r
 203                 m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");\r
 204                 m->mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");\r
 205                 m->mothurOut("The align.seqs command should be in the following format: \n");\r
 206                 m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");\r
 207                 m->mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");\r
 208                 m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");\r
 209         }\r
 210         catch(exception& e) {\r
 211                 m->errorOut(e, "AlignCommand", "help");\r
 212                 exit(1);\r
 213         }\r
 214 }\r
 215 \r
 216 \r
 217 //**********************************************************************************************************************\r
 218 \r
 219 int AlignCommand::execute(){\r
 220         try {\r
 221                 if (abort == true) {    return 0;       }\r
 222 \r
 223                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);\r
 224                 int longestBase = templateDB->getLongestBase();\r
 225                 \r
 226                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }\r
 227                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }\r
 228                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }\r
 229                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }\r
 230                 else {\r
 231                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");\r
 232                         m->mothurOutEndLine();\r
 233                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);\r
 234                 }\r
 235                 vector<string> outputNames;\r
 236                 \r
 237                 for (int s = 0; s < candidateFileNames.size(); s++) {\r
 238                         if (m->control_pressed) { return 0; }\r
 239                         \r
 240                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();\r
 241                         \r
 242                         if (outputDir == "") {  outputDir += hasPath(candidateFileNames[s]); }\r
 243                         string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";\r
 244                         string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";\r
 245                         string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";\r
 246                         bool hasAccnos = true;\r
 247                         \r
 248                         int numFastaSeqs = 0;\r
 249                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();\r
 250                         int start = time(NULL);\r
 251                 \r
 252 #ifdef USE_MPI  \r
 253                                 int pid, end, numSeqsPerProcessor; \r
 254                                 int tag = 2001;\r
 255                                 vector<long> MPIPos;\r
 256                                 MPIWroteAccnos = false;\r
 257                                 \r
 258                                 MPI_Status status; \r
 259                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are\r
 260                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); \r
 261 \r
 262                                 MPI_File inMPI;\r
 263                                 MPI_File outMPIAlign;\r
 264                                 MPI_File outMPIReport;\r
 265                                 MPI_File outMPIAccnos;\r
 266                                 \r
 267                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; \r
 268                                 int inMode=MPI_MODE_RDONLY; \r
 269                                 \r
 270                                 //char* outAlignFilename = new char[alignFileName.length()];\r
 271                                 //memcpy(outAlignFilename, alignFileName.c_str(), alignFileName.length());\r
 272                                 \r
 273                                 char outAlignFilename[1024];\r
 274                                 strcpy(outAlignFilename, alignFileName.c_str());\r
 275 \r
 276                                 //char* outReportFilename = new char[reportFileName.length()];\r
 277                                 //memcpy(outReportFilename, reportFileName.c_str(), reportFileName.length());\r
 278                                 \r
 279                                 char outReportFilename[1024];\r
 280                                 strcpy(outReportFilename, reportFileName.c_str());\r
 281 \r
 282                                 //char* outAccnosFilename = new char[accnosFileName.length()];\r
 283                                 //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());\r
 284                                 \r
 285                                 char outAccnosFilename[1024];\r
 286                                 strcpy(outAccnosFilename, accnosFileName.c_str());\r
 287 \r
 288                                 //char* inFileName = new char[candidateFileNames[s].length()];\r
 289                                 //memcpy(inFileName, candidateFileNames[s].c_str(), candidateFileNames[s].length());\r
 290                                 \r
 291                                 char inFileName[1024];\r
 292                                 strcpy(inFileName, candidateFileNames[s].c_str());\r
 293                                 \r
 294                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer\r
 295                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);\r
 296                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);\r
 297                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);\r
 298                                 \r
 299                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }\r
 300                                 \r
 301                                 if (pid == 0) { //you are the root process \r
 302                                         \r
 303                                         MPIPos = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs\r
 304                                         \r
 305                                         //send file positions to all processes\r
 306                                         for(int i = 1; i < processors; i++) { \r
 307                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);\r
 308                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);\r
 309                                         }\r
 310                                         \r
 311                                         //figure out how many sequences you have to align\r
 312                                         numSeqsPerProcessor = numFastaSeqs / processors;\r
 313                                         int startIndex =  pid * numSeqsPerProcessor;\r
 314                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }\r
 315                                         \r
 316                                 \r
 317                                         //align your part\r
 318                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);\r
 319                                         \r
 320                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }\r
 321 \r
 322                                         for (int i = 1; i < processors; i++) {\r
 323                                                 bool tempResult;\r
 324                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);\r
 325                                                 if (tempResult != 0) { MPIWroteAccnos = true; }\r
 326                                         }\r
 327                                 }else{ //you are a child process\r
 328                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);\r
 329                                         MPIPos.resize(numFastaSeqs+1);\r
 330                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);\r
 331 \r
 332                                         \r
 333                                         //figure out how many sequences you have to align\r
 334                                         numSeqsPerProcessor = numFastaSeqs / processors;\r
 335                                         int startIndex =  pid * numSeqsPerProcessor;\r
 336                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }\r
 337                                         \r
 338                                         \r
 339                                         //align your part\r
 340                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);\r
 341                                         \r
 342                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }\r
 343 \r
 344                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); \r
 345                                 }\r
 346                                 \r
 347                                 //close files \r
 348                                 MPI_File_close(&inMPI);\r
 349                                 MPI_File_close(&outMPIAlign);\r
 350                                 MPI_File_close(&outMPIReport);\r
 351                                 MPI_File_close(&outMPIAccnos);\r
 352                                 \r
 353                                 //delete accnos file if blank\r
 354                                 if (pid == 0) {\r
 355                                         //delete accnos file if its blank else report to user\r
 356                                         if (MPIWroteAccnos) { \r
 357                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");\r
 358                                                 if (!flip) {\r
 359                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); \r
 360                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }\r
 361                                                 m->mothurOutEndLine();\r
 362                                         }else { \r
 363                                                 //MPI_Info info;\r
 364                                                 //MPI_File_delete(outAccnosFilename, info);\r
 365                                                 hasAccnos = false;      \r
 366                                                 remove(accnosFileName.c_str()); \r
 367                                         }\r
 368                                 }\r
 369                                 \r
 370 #else\r
 371                         \r
 372         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
 373                         if(processors == 1){\r
 374                                 ifstream inFASTA;\r
 375                                 openInputFile(candidateFileNames[s], inFASTA);\r
 376                                 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');\r
 377                                 inFASTA.close();\r
 378                                 \r
 379                                 lines.push_back(new linePair(0, numFastaSeqs));\r
 380                                 \r
 381                                 driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);\r
 382                                 \r
 383                                 if (m->control_pressed) { \r
 384                                         remove(accnosFileName.c_str()); \r
 385                                         remove(alignFileName.c_str()); \r
 386                                         remove(reportFileName.c_str()); \r
 387                                         return 0; \r
 388                                 }\r
 389                                 \r
 390                                 //delete accnos file if its blank else report to user\r
 391                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }\r
 392                                 else { \r
 393                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");\r
 394                                         if (!flip) {\r
 395                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); \r
 396                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }\r
 397                                         m->mothurOutEndLine();\r
 398                                 }\r
 399                         }\r
 400                         else{\r
 401                                 vector<int> positions;\r
 402                                 processIDS.resize(0);\r
 403                                 \r
 404                                 ifstream inFASTA;\r
 405                                 openInputFile(candidateFileNames[s], inFASTA);\r
 406                                 \r
 407                                 string input;\r
 408                                 while(!inFASTA.eof()){\r
 409                                         input = getline(inFASTA);\r
 410                                         if (input.length() != 0) {\r
 411                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }\r
 412                                         }\r
 413                                 }\r
 414                                 inFASTA.close();\r
 415                                 \r
 416                                 numFastaSeqs = positions.size();\r
 417                                 \r
 418                                 int numSeqsPerProcessor = numFastaSeqs / processors;\r
 419                                 \r
 420                                 for (int i = 0; i < processors; i++) {\r
 421                                         long int startPos = positions[ i * numSeqsPerProcessor ];\r
 422                                         if(i == processors - 1){\r
 423                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;\r
 424                                         }\r
 425                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));\r
 426                                 }\r
 427                                 \r
 428                                 createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); \r
 429                                 \r
 430                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());\r
 431                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());\r
 432                                 \r
 433                                 //append alignment and report files\r
 434                                 for(int i=1;i<processors;i++){\r
 435                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);\r
 436                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());\r
 437                                         \r
 438                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);\r
 439                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());\r
 440                                 }\r
 441                                 \r
 442                                 vector<string> nonBlankAccnosFiles;\r
 443                                 //delete blank accnos files generated with multiple processes\r
 444                                 for(int i=0;i<processors;i++){  \r
 445                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {\r
 446                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");\r
 447                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }\r
 448                                 }\r
 449                                 \r
 450                                 //append accnos files\r
 451                                 if (nonBlankAccnosFiles.size() != 0) { \r
 452                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());\r
 453                                         \r
 454                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {\r
 455                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);\r
 456                                                 remove(nonBlankAccnosFiles[h].c_str());\r
 457                                         }\r
 458                                         m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");\r
 459                                         if (!flip) {\r
 460                                                 m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); \r
 461                                         }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }\r
 462                                         m->mothurOutEndLine();\r
 463                                 }else{ hasAccnos = false;  }\r
 464                                 \r
 465                                 if (m->control_pressed) { \r
 466                                         remove(accnosFileName.c_str()); \r
 467                                         remove(alignFileName.c_str()); \r
 468                                         remove(reportFileName.c_str()); \r
 469                                         return 0; \r
 470                                 }\r
 471                         }\r
 472         #else\r
 473                         ifstream inFASTA;\r
 474                         openInputFile(candidateFileNames[s], inFASTA);\r
 475                         numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');\r
 476                         inFASTA.close();\r
 477                         \r
 478                         lines.push_back(new linePair(0, numFastaSeqs));\r
 479                         \r
 480                         driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);\r
 481                         \r
 482                         if (m->control_pressed) { \r
 483                                 remove(accnosFileName.c_str()); \r
 484                                 remove(alignFileName.c_str()); \r
 485                                 remove(reportFileName.c_str()); \r
 486                                 return 0; \r
 487                         }\r
 488                         \r
 489                         //delete accnos file if its blank else report to user\r
 490                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }\r
 491                         else { \r
 492                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");\r
 493                                 if (!flip) {\r
 494                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); \r
 495                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }\r
 496                                 m->mothurOutEndLine();\r
 497                         }\r
 498                         \r
 499         #endif\r
 500 \r
 501 #endif          \r
 502 \r
 503 \r
 504                 #ifdef USE_MPI\r
 505                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); \r
 506                                         \r
 507                         if (pid == 0) { //only one process should output to screen\r
 508                 #endif\r
 509 \r
 510                         outputNames.push_back(alignFileName);\r
 511                         outputNames.push_back(reportFileName);\r
 512                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);          }\r
 513                         \r
 514                 #ifdef USE_MPI\r
 515                         }\r
 516                 #endif\r
 517 \r
 518                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");\r
 519                         m->mothurOutEndLine();\r
 520                         m->mothurOutEndLine();\r
 521                 }\r
 522                 \r
 523                 \r
 524                 m->mothurOutEndLine();\r
 525                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();\r
 526                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }\r
 527                 m->mothurOutEndLine();\r
 528 \r
 529                 return 0;\r
 530         }\r
 531         catch(exception& e) {\r
 532                 m->errorOut(e, "AlignCommand", "execute");\r
 533                 exit(1);\r
 534         }\r
 535 }\r
 536 \r
 537 //**********************************************************************************************************************\r
 538 \r
 539 int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){\r
 540         try {\r
 541                 ofstream alignmentFile;\r
 542                 openOutputFile(alignFName, alignmentFile);\r
 543                 \r
 544                 ofstream accnosFile;\r
 545                 openOutputFile(accnosFName, accnosFile);\r
 546                 \r
 547                 NastReport report(reportFName);\r
 548                 \r
 549                 ifstream inFASTA;\r
 550                 openInputFile(filename, inFASTA);\r
 551 \r
 552                 inFASTA.seekg(line->start);\r
 553         \r
 554                 for(int i=0;i<line->numSeqs;i++){\r
 555                         \r
 556                         if (m->control_pressed) {  return 0; }\r
 557                         \r
 558                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);\r
 559         \r
 560                         int origNumBases = candidateSeq->getNumBases();\r
 561                         string originalUnaligned = candidateSeq->getUnaligned();\r
 562                         int numBasesNeeded = origNumBases * threshold;\r
 563         \r
 564                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file\r
 565                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {\r
 566                                         alignment->resize(candidateSeq->getUnaligned().length()+1);\r
 567                                 }\r
 568                                                                 \r
 569                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);\r
 570                                 Sequence* templateSeq = &temp;\r
 571                                 \r
 572                                 float searchScore = templateDB->getSearchScore();\r
 573                                                                 \r
 574                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);\r
 575                                 Sequence* copy;\r
 576                                 \r
 577                                 Nast* nast2;\r
 578                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below\r
 579                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below\r
 580                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place\r
 581                                                                                                 //so this bool tells you if you need to delete it\r
 582                                                                                                 \r
 583                                 //if there is a possibility that this sequence should be reversed\r
 584                                 if (candidateSeq->getNumBases() < numBasesNeeded) {\r
 585                                         \r
 586                                         string wasBetter = "";\r
 587                                         //if the user wants you to try the reverse\r
 588                                         if (flip) {\r
 589                                                 //get reverse compliment\r
 590                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);\r
 591                                                 copy->reverseComplement();\r
 592                                                 \r
 593                                                 //rerun alignment\r
 594                                                 Sequence temp2 = templateDB->findClosestSequence(copy);\r
 595                                                 Sequence* templateSeq2 = &temp2;\r
 596                                                 \r
 597                                                 searchScore = templateDB->getSearchScore();\r
 598                                                 \r
 599                                                 nast2 = new Nast(alignment, copy, templateSeq2);\r
 600                         \r
 601                                                 //check if any better\r
 602                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {\r
 603                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better\r
 604                                                         templateSeq = templateSeq2; \r
 605                                                         delete nast;\r
 606                                                         nast = nast2;\r
 607                                                         needToDeleteCopy = true;\r
 608                                                 }else{  \r
 609                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";\r
 610                                                         delete nast2;\r
 611                                                         delete copy;    \r
 612                                                 }\r
 613                                         }\r
 614                                         \r
 615                                         //create accnos file with names\r
 616                                         accnosFile << candidateSeq->getName() << wasBetter << endl;\r
 617                                 }\r
 618                                 \r
 619                                 report.setCandidate(candidateSeq);\r
 620                                 report.setTemplate(templateSeq);\r
 621                                 report.setSearchParameters(search, searchScore);\r
 622                                 report.setAlignmentParameters(align, alignment);\r
 623                                 report.setNastParameters(*nast);\r
 624         \r
 625                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;\r
 626                                 \r
 627                                 report.print();\r
 628                                 delete nast;\r
 629                                 if (needToDeleteCopy) {   delete copy;   }\r
 630                         }\r
 631                         delete candidateSeq;\r
 632                         \r
 633                         //report progress\r
 634                         if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }\r
 635                 }\r
 636                 //report progress\r
 637                 if((line->numSeqs) % 100 != 0){ m->mothurOut(toString(line->numSeqs)); m->mothurOutEndLine();           }\r
 638                 \r
 639                 alignmentFile.close();\r
 640                 inFASTA.close();\r
 641                 accnosFile.close();\r
 642                 \r
 643                 return 1;\r
 644         }\r
 645         catch(exception& e) {\r
 646                 m->errorOut(e, "AlignCommand", "driver");\r
 647                 exit(1);\r
 648         }\r
 649 }\r
 650 //**********************************************************************************************************************\r
 651 #ifdef USE_MPI\r
 652 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<long>& MPIPos){\r
 653         try {\r
 654                 string outputString = "";\r
 655                 MPI_Status statusReport; \r
 656                 MPI_Status statusAlign; \r
 657                 MPI_Status statusAccnos; \r
 658                 MPI_Status status; \r
 659                 int pid;\r
 660                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are\r
 661         \r
 662                 NastReport report;\r
 663                 \r
 664                 if (pid == 0) {\r
 665                         outputString = report.getHeaders();\r
 666                         int length = outputString.length();\r
 667             \r
 668                         char* buf = new char[length];\r
 669                         memcpy(buf, outputString.c_str(), length);\r
 670                 \r
 671                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);\r
 672 \r
 673             delete buf;\r
 674                 }\r
 675                 \r
 676                 for(int i=0;i<num;i++){\r
 677                 \r
 678                         if (m->control_pressed) {  return 0; }\r
 679 \r
 680                         //read next sequence\r
 681                         int length = MPIPos[start+i+1] - MPIPos[start+i];\r
 682 \r
 683                         char* buf4 = new char[length];\r
 684                         memcpy(buf4, outputString.c_str(), length);\r
 685 \r
 686                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);\r
 687                         \r
 688                         string tempBuf = buf4;\r
 689 \r
 690                         delete buf4;\r
 691 \r
 692                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }\r
 693                         istringstream iss (tempBuf,istringstream::in);\r
 694         \r
 695                         Sequence* candidateSeq = new Sequence(iss);  \r
 696                         int origNumBases = candidateSeq->getNumBases();\r
 697                         string originalUnaligned = candidateSeq->getUnaligned();\r
 698                         int numBasesNeeded = origNumBases * threshold;\r
 699         \r
 700                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file\r
 701                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {\r
 702                                         alignment->resize(candidateSeq->getUnaligned().length()+1);\r
 703                                 }\r
 704                                                                 \r
 705                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);\r
 706                                 Sequence* templateSeq = &temp;\r
 707                                 \r
 708                                 float searchScore = templateDB->getSearchScore();\r
 709                                                                 \r
 710                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);\r
 711                                 Sequence* copy;\r
 712                                 \r
 713                                 Nast* nast2;\r
 714                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below\r
 715                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below\r
 716                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place\r
 717                                                                                                 //so this bool tells you if you need to delete it\r
 718                                                                                                 \r
 719                                 //if there is a possibility that this sequence should be reversed\r
 720                                 if (candidateSeq->getNumBases() < numBasesNeeded) {\r
 721                                         \r
 722                                         string wasBetter = "";\r
 723                                         //if the user wants you to try the reverse\r
 724                                         if (flip) {\r
 725                                                 //get reverse compliment\r
 726                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);\r
 727                                                 copy->reverseComplement();\r
 728                                                 \r
 729                                                 //rerun alignment\r
 730                                                 Sequence temp2 = templateDB->findClosestSequence(copy);\r
 731                                                 Sequence* templateSeq2 = &temp2;\r
 732                                                 \r
 733                                                 searchScore = templateDB->getSearchScore();\r
 734                                                 \r
 735                                                 nast2 = new Nast(alignment, copy, templateSeq2);\r
 736                         \r
 737                                                 //check if any better\r
 738                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {\r
 739                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better\r
 740                                                         templateSeq = templateSeq2; \r
 741                                                         delete nast;\r
 742                                                         nast = nast2;\r
 743                                                         needToDeleteCopy = true;\r
 744                                                 }else{  \r
 745                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";\r
 746                                                         delete nast2;\r
 747                                                         delete copy;    \r
 748                                                 }\r
 749                                         }\r
 750                                         \r
 751                                         //create accnos file with names\r
 752                                         outputString = candidateSeq->getName() + wasBetter + "\n";\r
 753                                         \r
 754                                         //send results to parent\r
 755                                         int length = outputString.length();\r
 756 \r
 757                                         char* buf = new char[length];\r
 758                                         memcpy(buf, outputString.c_str(), length);\r
 759                                 \r
 760                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);\r
 761                                         delete buf;\r
 762                                         MPIWroteAccnos = true;\r
 763                                 }\r
 764                                 \r
 765                                 report.setCandidate(candidateSeq);\r
 766                                 report.setTemplate(templateSeq);\r
 767                                 report.setSearchParameters(search, searchScore);\r
 768                                 report.setAlignmentParameters(align, alignment);\r
 769                                 report.setNastParameters(*nast);\r
 770         \r
 771                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";\r
 772                                 \r
 773                                 //send results to parent\r
 774                                 int length = outputString.length();\r
 775                                 char* buf2 = new char[length];\r
 776                                 memcpy(buf2, outputString.c_str(), length);\r
 777                                 \r
 778                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);\r
 779                                 \r
 780                                 delete buf2;\r
 781 \r
 782                                 outputString = report.getReport();\r
 783                                 \r
 784                                 //send results to parent\r
 785                                 length = outputString.length();\r
 786                                 char* buf3 = new char[length];\r
 787                                 memcpy(buf3, outputString.c_str(), length);\r
 788                                 \r
 789                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);\r
 790                                 \r
 791                                 delete buf3;\r
 792                                 delete nast;\r
 793                                 if (needToDeleteCopy) {   delete copy;   }\r
 794                         }\r
 795                         delete candidateSeq;\r
 796                         \r
 797                         //report progress\r
 798                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }\r
 799                 }\r
 800                 //report progress\r
 801                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }\r
 802                 \r
 803                 return 1;\r
 804         }\r
 805         catch(exception& e) {\r
 806                 m->errorOut(e, "AlignCommand", "driverMPI");\r
 807                 exit(1);\r
 808         }\r
 809 }\r
 810 #endif\r
 811 /**************************************************************************************************/\r
 812 \r
 813 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {\r
 814         try {\r
 815 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
 816                 int process = 0;\r
 817                 int exitCommand = 1;\r
 818                 //              processIDS.resize(0);\r
 819                 \r
 820                 //loop through and create all the processes you want\r
 821                 while (process != processors) {\r
 822                         int pid = fork();\r
 823                         \r
 824                         if (pid > 0) {\r
 825                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later\r
 826                                 process++;\r
 827                         }else if (pid == 0){\r
 828                                 exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);\r
 829                                 exit(0);\r
 830                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }\r
 831                 }\r
 832                 \r
 833                 //force parent to wait until all the processes are done\r
 834                 for (int i=0;i<processors;i++) { \r
 835                         int temp = processIDS[i];\r
 836                         wait(&temp);\r
 837                 }\r
 838                 \r
 839                 return exitCommand;\r
 840 #endif          \r
 841         }\r
 842         catch(exception& e) {\r
 843                 m->errorOut(e, "AlignCommand", "createProcesses");\r
 844                 exit(1);\r
 845         }\r
 846 }\r
 847 \r
 848 /**************************************************************************************************/\r
 849 \r
 850 void AlignCommand::appendAlignFiles(string temp, string filename) {\r
 851         try{\r
 852                 \r
 853                 ofstream output;\r
 854                 ifstream input;\r
 855                 openOutputFileAppend(filename, output);\r
 856                 openInputFile(temp, input);\r
 857                 \r
 858                 while(char c = input.get()){\r
 859                         if(input.eof())         {       break;                  }\r
 860                         else                            {       output << c;    }\r
 861                 }\r
 862                 \r
 863                 input.close();\r
 864                 output.close();\r
 865         }\r
 866         catch(exception& e) {\r
 867                 m->errorOut(e, "AlignCommand", "appendAlignFiles");\r
 868                 exit(1);\r
 869         }\r
 870 }\r
 871 //**********************************************************************************************************************\r
 872 \r
 873 void AlignCommand::appendReportFiles(string temp, string filename) {\r
 874         try{\r
 875                 \r
 876                 ofstream output;\r
 877                 ifstream input;\r
 878                 openOutputFileAppend(filename, output);\r
 879                 openInputFile(temp, input);\r
 880 \r
 881                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line\r
 882                                 \r
 883                 while(char c = input.get()){\r
 884                         if(input.eof())         {       break;                  }\r
 885                         else                            {       output << c;    }\r
 886                 }\r
 887                 \r
 888                 input.close();\r
 889                 output.close();\r
 890         }\r
 891         catch(exception& e) {\r
 892                 m->errorOut(e, "AlignCommand", "appendReportFiles");\r
 893                 exit(1);\r
 894         }\r
 895 }\r
 896 //**********************************************************************************************************************\r