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