seqsummarycommand.cpp

   1 /*
   2  *  seqcoordcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 5/30/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "seqsummarycommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14 vector<string> SeqSummaryCommand::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "SeqSummaryCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string SeqSummaryCommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 helpString += "The summary.seqs command reads a fastafile and summarizes the sequences.\n";
  36                 helpString += "The summary.seqs command parameters are fasta, name and processors, fasta is required, unless you have a valid current fasta file.\n";
  37                 helpString += "The name parameter allows you to enter a name file associated with your fasta file. \n";
  38                 helpString += "The summary.seqs command should be in the following format: \n";
  39                 helpString += "summary.seqs(fasta=yourFastaFile, processors=2) \n";
  40                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  41                 return helpString;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "SeqSummaryCommand", "getHelpString");
  45                 exit(1);
  46         }
  47 }
  48
  49 //**********************************************************************************************************************
  50 SeqSummaryCommand::SeqSummaryCommand(){
  51         try {
  52                 abort = true; calledHelp = true;
  53                 setParameters();
  54                 vector<string> tempOutNames;
  55                 outputTypes["summary"] = tempOutNames;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
  59                 exit(1);
  60         }
  61 }
  62 //***************************************************************************************************************
  63
  64 SeqSummaryCommand::SeqSummaryCommand(string option)  {
  65         try {
  66                 abort = false; calledHelp = false;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; calledHelp = true; }
  70                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  71
  72                 else {
  73                         vector<string> myArray = setParameters();
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter("summary.seqs");
  79                         map<string,string>::iterator it;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //if the user changes the input directory command factory will send this info to us in the output parameter
  87                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  88                         if (inputDir == "not found"){   inputDir = "";          }
  89                         else {
  90                                 string path;
  91                                 it = parameters.find("fasta");
  92                                 //user has given a template file
  93                                 if(it != parameters.end()){
  94                                         path = m->hasPath(it->second);
  95                                         //if the user has not given a path then, add inputdir. else leave path alone.
  96                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  97                                 }
  98
  99                                 it = parameters.find("name");
 100                                 //user has given a template file
 101                                 if(it != parameters.end()){
 102                                         path = m->hasPath(it->second);
 103                                         //if the user has not given a path then, add inputdir. else leave path alone.
 104                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 105                                 }
 106                         }
 107
 108                         //initialize outputTypes
 109                         vector<string> tempOutNames;
 110                         outputTypes["summary"] = tempOutNames;
 111
 112                         //check for required parameters
 113                         fastafile = validParameter.validFile(parameters, "fasta", true);
 114                         if (fastafile == "not open") { abort = true; }
 115                         else if (fastafile == "not found") {
 116                                 fastafile = m->getFastaFile();
 117                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 118                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 119                         }else { m->setFastaFile(fastafile); }
 120
 121                         namefile = validParameter.validFile(parameters, "name", true);
 122                         if (namefile == "not open") { namefile = ""; abort = true; }
 123                         else if (namefile == "not found") { namefile = "";  }
 124                         else { m->setNameFile(namefile); }
 125
 126                         //if the user changes the output directory command factory will send this info to us in the output parameter
 127                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 128                                 outputDir = "";
 129                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 130                         }
 131
 132                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 133                         m->setProcessors(temp);
 134                         convert(temp, processors);
 135
 136
 137                 }
 138         }
 139         catch(exception& e) {
 140                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
 141                 exit(1);
 142         }
 143 }
 144 //***************************************************************************************************************
 145
 146 int SeqSummaryCommand::execute(){
 147         try{
 148
 149                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 150
 151                 //set current fasta to fastafile
 152                 m->setFastaFile(fastafile);
 153
 154                 string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
 155
 156                 int numSeqs = 0;
 157
 158                 vector<int> startPosition;
 159                 vector<int> endPosition;
 160                 vector<int> seqLength;
 161                 vector<int> ambigBases;
 162                 vector<int> longHomoPolymer;
 163
 164                 if (namefile != "") { nameMap = m->readNames(namefile); }
 165
 166                 if (m->control_pressed) { return 0; }
 167
 168 #ifdef USE_MPI
 169                                 int pid, numSeqsPerProcessor;
 170                                 int tag = 2001;
 171                                 int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
 172                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 173                                 vector<unsigned long long> MPIPos;
 174
 175                                 MPI_Status status;
 176                                 MPI_Status statusOut;
 177                                 MPI_File inMPI;
 178                                 MPI_File outMPI;
 179                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 180                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 181
 182                                 char tempFileName[1024];
 183                                 strcpy(tempFileName, fastafile.c_str());
 184
 185                                 char sumFileName[1024];
 186                                 strcpy(sumFileName, summaryFile.c_str());
 187
 188                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 189                                 MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI);
 190
 191                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); return 0;  }
 192
 193                                 if (pid == 0) { //you are the root process
 194                                                 //print header
 195                                                 string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs\n";
 196                                                 int length = outputString.length();
 197                                                 char* buf2 = new char[length];
 198                                                 memcpy(buf2, outputString.c_str(), length);
 199
 200                                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
 201                                                 delete buf2;
 202
 203                                                 MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 204
 205                                                 for(int i = 1; i < processors; i++) {
 206                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 207                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 208                                                 }
 209
 210                                                 //figure out how many sequences you have to do
 211                                                 numSeqsPerProcessor = numSeqs / processors;
 212                                                 int startIndex =  pid * numSeqsPerProcessor;
 213                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 214
 215                                                 //do your part
 216                                                 MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 217
 218                                 }else { //i am the child process
 219
 220                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 221                                         MPIPos.resize(numSeqs+1);
 222                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 223
 224                                         //figure out how many sequences you have to align
 225                                         numSeqsPerProcessor = numSeqs / processors;
 226                                         int startIndex =  pid * numSeqsPerProcessor;
 227                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 228
 229                                         //do your part
 230                                         MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 231                                 }
 232
 233                                 MPI_File_close(&inMPI);
 234                                 MPI_File_close(&outMPI);
 235                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 236
 237                                 if (pid == 0) {
 238                                         //get the info from the child processes
 239                                         for(int i = 1; i < processors; i++) {
 240                                                 int size;
 241                                                 MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 242
 243                                                 vector<int> temp; temp.resize(size+1);
 244
 245                                                 for(int j = 0; j < 5; j++) {
 246
 247                                                         MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 248                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
 249
 250                                                         if (receiveTag == startTag) {
 251                                                                 for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
 252                                                         }else if (receiveTag == endTag) {
 253                                                                 for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
 254                                                         }else if (receiveTag == lengthTag) {
 255                                                                 for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
 256                                                         }else if (receiveTag == baseTag) {
 257                                                                 for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
 258                                                         }else if (receiveTag == lhomoTag) {
 259                                                                 for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
 260                                                         }
 261                                                 }
 262                                         }
 263
 264                                 }else{
 265
 266                                         //send my counts
 267                                         int size = startPosition.size();
 268                                         MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 269
 270                                         startPosition.push_back(startTag);
 271                                         int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 272                                         endPosition.push_back(endTag);
 273                                         ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 274                                         seqLength.push_back(lengthTag);
 275                                         ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 276                                         ambigBases.push_back(baseTag);
 277                                         ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 278                                         longHomoPolymer.push_back(lhomoTag);
 279                                         ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 280                                 }
 281
 282                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 283 #else
 284                         vector<unsigned long long> positions;
 285                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 286                                 positions = m->divideFile(fastafile, processors);
 287                                 for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 288                         #else
 289                                 positions = m->setFilePosFasta(fastafile, numSeqs);
 290
 291                                 //figure out how many sequences you have to process
 292                                 int numSeqsPerProcessor = numSeqs / processors;
 293                                 for (int i = 0; i < processors; i++) {
 294                                         int startIndex =  i * numSeqsPerProcessor;
 295                                         if(i == (processors - 1)){      numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 296                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 297                                 }
 298                         #endif
 299
 300
 301                         if(processors == 1){
 302                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 303                         }else{
 304                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
 305                         }
 306
 307                         if (m->control_pressed) {  return 0; }
 308 #endif
 309
 310                 #ifdef USE_MPI
 311                         if (pid == 0) {
 312                 #endif
 313
 314                 sort(startPosition.begin(), startPosition.end());
 315                 sort(endPosition.begin(), endPosition.end());
 316                 sort(seqLength.begin(), seqLength.end());
 317                 sort(ambigBases.begin(), ambigBases.end());
 318                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 319                 int size = startPosition.size();
 320
 321                 //find means
 322                 float meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
 323                 meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
 324                 for (int i = 0; i < size; i++) {
 325                         meanStartPosition += startPosition[i];
 326                         meanEndPosition += endPosition[i];
 327                         meanSeqLength += seqLength[i];
 328                         meanAmbigBases += ambigBases[i];
 329                         meanLongHomoPolymer += longHomoPolymer[i];
 330                 }
 331                 //this is an int divide so the remainder is lost
 332                 meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
 333
 334                 int ptile0_25   = int(size * 0.025);
 335                 int ptile25             = int(size * 0.250);
 336                 int ptile50             = int(size * 0.500);
 337                 int ptile75             = int(size * 0.750);
 338                 int ptile97_5   = int(size * 0.975);
 339                 int ptile100    = size - 1;
 340
 341                 //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
 342                 if (startPosition[0] == -1) {  startPosition[0] = 0;    }
 343                 if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
 344
 345                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 346
 347                 m->mothurOutEndLine();
 348                 m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine();
 349                 m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0]) + "\t" + toString(1)); m->mothurOutEndLine();
 350                 m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25]) + "\t" + toString(ptile0_25+1)); m->mothurOutEndLine();
 351                 m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25]) + "\t" + toString(ptile25+1)); m->mothurOutEndLine();
 352                 m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50]) + "\t" + toString(ptile50+1)); m->mothurOutEndLine();
 353                 m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine();
 354                 m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine();
 355                 m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine();
 356                 m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
 357
 358                 if (namefile == "") {  m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
 359                 else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
 360
 361                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 362
 363                 m->mothurOutEndLine();
 364                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 365                 m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
 366                 m->mothurOutEndLine();
 367
 368                 #ifdef USE_MPI
 369                         }
 370                 #endif
 371
 372                 return 0;
 373         }
 374         catch(exception& e) {
 375                 m->errorOut(e, "SeqSummaryCommand", "execute");
 376                 exit(1);
 377         }
 378 }
 379 /**************************************************************************************/
 380 int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
 381         try {
 382
 383                 ofstream outSummary;
 384                 m->openOutputFile(sumFile, outSummary);
 385
 386                 //print header if you are process 0
 387                 if (filePos->start == 0) {
 388                         outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
 389                 }
 390
 391                 ifstream in;
 392                 m->openInputFile(filename, in);
 393
 394                 in.seekg(filePos->start);
 395
 396                 bool done = false;
 397                 int count = 0;
 398
 399                 while (!done) {
 400
 401                         if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
 402
 403                         Sequence current(in); m->gobble(in);
 404
 405                         if (current.getName() != "") {
 406
 407                                 int num = 1;
 408                                 if (namefile != "") {
 409                                         //make sure this sequence is in the namefile, else error
 410                                         map<string, int>::iterator it = nameMap.find(current.getName());
 411
 412                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 413                                         else { num = it->second; }
 414                                 }
 415
 416                                 //for each sequence this sequence represents
 417                                 for (int i = 0; i < num; i++) {
 418                                         startPosition.push_back(current.getStartPos());
 419                                         endPosition.push_back(current.getEndPos());
 420                                         seqLength.push_back(current.getNumBases());
 421                                         ambigBases.push_back(current.getAmbigBases());
 422                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 423                                 }
 424
 425                                 count++;
 426                                 outSummary << current.getName() << '\t';
 427                                 outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
 428                                 outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
 429                                 outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
 430                         }
 431
 432                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 433                                 unsigned long long pos = in.tellg();
 434                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 435                         #else
 436                                 if (in.eof()) { break; }
 437                         #endif
 438
 439                         //report progress
 440                         //if((count) % 100 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 441                 }
 442                 //report progress
 443                 //if((count) % 100 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 444
 445                 in.close();
 446
 447                 return count;
 448         }
 449         catch(exception& e) {
 450                 m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
 451                 exit(1);
 452         }
 453 }
 454 #ifdef USE_MPI
 455 /**************************************************************************************/
 456 int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
 457         try {
 458
 459                 int pid;
 460                 MPI_Status status;
 461                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 462
 463                 for(int i=0;i<num;i++){
 464
 465                         if (m->control_pressed) { return 0; }
 466
 467                         //read next sequence
 468                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 469
 470                         char* buf4 = new char[length];
 471                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 472
 473                         string tempBuf = buf4;
 474                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 475                         istringstream iss (tempBuf,istringstream::in);
 476                         delete buf4;
 477
 478                         Sequence current(iss);
 479
 480                         if (current.getName() != "") {
 481
 482                                 int num = 1;
 483                                 if (namefile != "") {
 484                                         //make sure this sequence is in the namefile, else error
 485                                         map<string, int>::iterator it = nameMap.find(current.getName());
 486
 487                                         if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; }
 488                                         else { num = it->second; }
 489                                 }
 490
 491                                 //for each sequence this sequence represents
 492                                 for (int i = 0; i < num; i++) {
 493                                         startPosition.push_back(current.getStartPos());
 494                                         endPosition.push_back(current.getEndPos());
 495                                         seqLength.push_back(current.getNumBases());
 496                                         ambigBases.push_back(current.getAmbigBases());
 497                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 498                                 }
 499
 500                                 string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
 501                                 outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n";
 502
 503                                 //output to file
 504                                 length = outputString.length();
 505                                 char* buf3 = new char[length];
 506                                 memcpy(buf3, outputString.c_str(), length);
 507
 508                                 MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
 509                                 delete buf3;
 510                         }
 511                 }
 512
 513                 return 0;
 514         }
 515         catch(exception& e) {
 516                 m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
 517                 exit(1);
 518         }
 519 }
 520 #endif
 521 /**************************************************************************************************/
 522 int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
 523         try {
 524                 int process = 1;
 525                 int num = 0;
 526                 processIDS.clear();
 527
 528 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 529
 530                 //loop through and create all the processes you want
 531                 while (process != processors) {
 532                         int pid = fork();
 533
 534                         if (pid > 0) {
 535                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 536                                 process++;
 537                         }else if (pid == 0){
 538                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
 539
 540                                 //pass numSeqs to parent
 541                                 ofstream out;
 542                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 543                                 m->openOutputFile(tempFile, out);
 544
 545                                 out << num << endl;
 546                                 out << startPosition.size() << endl;
 547                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 548                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 549                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 550                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 551                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 552
 553                                 out.close();
 554
 555                                 exit(0);
 556                         }else {
 557                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 558                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 559                                 exit(0);
 560                         }
 561                 }
 562
 563                 //do your part
 564                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile, lines[0]);
 565
 566                 //force parent to wait until all the processes are done
 567                 for (int i=0;i<processIDS.size();i++) {
 568                         int temp = processIDS[i];
 569                         wait(&temp);
 570                 }
 571
 572                 //parent reads in and combine Filter info
 573                 for (int i = 0; i < processIDS.size(); i++) {
 574                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 575                         ifstream in;
 576                         m->openInputFile(tempFilename, in);
 577
 578                         int temp, tempNum;
 579                         in >> tempNum; m->gobble(in); num += tempNum;
 580                         in >> tempNum; m->gobble(in);
 581                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 582                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 583                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 584                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 585                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 586
 587                         in.close();
 588                         m->mothurRemove(tempFilename);
 589
 590                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 591                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 592                 }
 593
 594 #else
 595                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 596                 //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
 597                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 598                 //Taking advantage of shared memory to allow both threads to add info to vectors.
 599                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 600
 601                 vector<seqSumData*> pDataArray;
 602                 DWORD   dwThreadIdArray[processors];
 603                 HANDLE  hThreadArray[processors];
 604
 605                 //Create processor worker threads.
 606                 for( int i=0; i<processors; i++ ){
 607
 608                         //cout << i << '\t' << lines[i]->start << '\t' << lines[i]->end << endl;
 609                         // Allocate memory for thread data.
 610                         seqSumData* tempSum = new seqSumData(&startPosition, &endPosition, &seqLength, &ambigBases, &longHomoPolymer, filename, (sumFile + toString(i) + ".temp"), m, lines[i]->start, lines[i]->end, namefile, nameMap);
 611                         pDataArray.push_back(tempSum);
 612                         processIDS.push_back(i);
 613
 614                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 615                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 616                         hThreadArray[i] = CreateThread(NULL, 0, MySeqSumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 617                 }
 618
 619                 //Wait until all threads have terminated.
 620                 WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
 621
 622                 //Close all thread handles and free memory allocations.
 623                 for(int i=0; i < pDataArray.size(); i++){
 624                         num += pDataArray[i]->count;
 625                         CloseHandle(hThreadArray[i]);
 626                         delete pDataArray[i];
 627                 }
 628
 629                 //rename((sumFile + toString(processIDS[0]) + ".temp").c_str(), sumFile.c_str());
 630                 //append files
 631                 for(int i=0;i<processIDS.size();i++){
 632                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 633                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 634                 }
 635 #endif
 636                 return num;
 637         }
 638         catch(exception& e) {
 639                 m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
 640                 exit(1);
 641         }
 642 }
 643 /**********************************************************************************************************************/
 644
 645
 646