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                         m->mothurConvert(temp, processors);
 135
 136                         if (namefile == "") {
 137                                 vector<string> files; files.push_back(fastafile);
 138                                 parser.getNameFile(files);
 139                         }
 140
 141                 }
 142         }
 143         catch(exception& e) {
 144                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
 145                 exit(1);
 146         }
 147 }
 148 //***************************************************************************************************************
 149
 150 int SeqSummaryCommand::execute(){
 151         try{
 152
 153                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 154
 155                 //set current fasta to fastafile
 156                 m->setFastaFile(fastafile);
 157
 158                 string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
 159
 160                 int numSeqs = 0;
 161
 162                 vector<int> startPosition;
 163                 vector<int> endPosition;
 164                 vector<int> seqLength;
 165                 vector<int> ambigBases;
 166                 vector<int> longHomoPolymer;
 167
 168                 if (namefile != "") { nameMap = m->readNames(namefile); }
 169
 170                 if (m->control_pressed) { return 0; }
 171
 172 #ifdef USE_MPI
 173                                 int pid, numSeqsPerProcessor;
 174                                 int tag = 2001;
 175                                 int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
 176                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 177                                 vector<unsigned long long> MPIPos;
 178
 179                                 MPI_Status status;
 180                                 MPI_Status statusOut;
 181                                 MPI_File inMPI;
 182                                 MPI_File outMPI;
 183                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 184                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 185
 186                                 char tempFileName[1024];
 187                                 strcpy(tempFileName, fastafile.c_str());
 188
 189                                 char sumFileName[1024];
 190                                 strcpy(sumFileName, summaryFile.c_str());
 191
 192                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 193                                 MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI);
 194
 195                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); return 0;  }
 196
 197                                 if (pid == 0) { //you are the root process
 198                                                 //print header
 199                                                 string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs\n";
 200                                                 int length = outputString.length();
 201                                                 char* buf2 = new char[length];
 202                                                 memcpy(buf2, outputString.c_str(), length);
 203
 204                                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
 205                                                 delete buf2;
 206
 207                                                 MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 208
 209                                                 for(int i = 1; i < processors; i++) {
 210                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 211                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 212                                                 }
 213
 214                                                 //figure out how many sequences you have to do
 215                                                 numSeqsPerProcessor = numSeqs / processors;
 216                                                 int startIndex =  pid * numSeqsPerProcessor;
 217                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 218
 219                                                 //do your part
 220                                                 MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 221
 222                                 }else { //i am the child process
 223
 224                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 225                                         MPIPos.resize(numSeqs+1);
 226                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 227
 228                                         //figure out how many sequences you have to align
 229                                         numSeqsPerProcessor = numSeqs / processors;
 230                                         int startIndex =  pid * numSeqsPerProcessor;
 231                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 232
 233                                         //do your part
 234                                         MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 235                                 }
 236
 237                                 MPI_File_close(&inMPI);
 238                                 MPI_File_close(&outMPI);
 239                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 240
 241                                 if (pid == 0) {
 242                                         //get the info from the child processes
 243                                         for(int i = 1; i < processors; i++) {
 244                                                 int size;
 245                                                 MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 246
 247                                                 vector<int> temp; temp.resize(size+1);
 248
 249                                                 for(int j = 0; j < 5; j++) {
 250
 251                                                         MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 252                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
 253
 254                                                         if (receiveTag == startTag) {
 255                                                                 for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
 256                                                         }else if (receiveTag == endTag) {
 257                                                                 for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
 258                                                         }else if (receiveTag == lengthTag) {
 259                                                                 for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
 260                                                         }else if (receiveTag == baseTag) {
 261                                                                 for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
 262                                                         }else if (receiveTag == lhomoTag) {
 263                                                                 for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
 264                                                         }
 265                                                 }
 266                                         }
 267
 268                                 }else{
 269
 270                                         //send my counts
 271                                         int size = startPosition.size();
 272                                         MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 273
 274                                         startPosition.push_back(startTag);
 275                                         int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 276                                         endPosition.push_back(endTag);
 277                                         ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 278                                         seqLength.push_back(lengthTag);
 279                                         ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 280                                         ambigBases.push_back(baseTag);
 281                                         ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 282                                         longHomoPolymer.push_back(lhomoTag);
 283                                         ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 284                                 }
 285
 286                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 287 #else
 288                         vector<unsigned long long> positions;
 289                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 290                                 positions = m->divideFile(fastafile, processors);
 291                                 for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 292                         #else
 293                                 positions = m->setFilePosFasta(fastafile, numSeqs);
 294                 if (positions.size() < processors) { processors = positions.size(); }
 295
 296                                 //figure out how many sequences you have to process
 297                                 int numSeqsPerProcessor = numSeqs / processors;
 298                                 for (int i = 0; i < processors; i++) {
 299                                         int startIndex =  i * numSeqsPerProcessor;
 300                                         if(i == (processors - 1)){      numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 301                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 302                                 }
 303                         #endif
 304
 305
 306                         if(processors == 1){
 307                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 308                         }else{
 309                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
 310                         }
 311
 312                         if (m->control_pressed) {  return 0; }
 313 #endif
 314
 315                 #ifdef USE_MPI
 316                         if (pid == 0) {
 317                 #endif
 318
 319                 sort(startPosition.begin(), startPosition.end());
 320                 sort(endPosition.begin(), endPosition.end());
 321                 sort(seqLength.begin(), seqLength.end());
 322                 sort(ambigBases.begin(), ambigBases.end());
 323                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 324                 int size = startPosition.size();
 325
 326                 //find means
 327                 float meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
 328                 meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
 329                 for (int i = 0; i < size; i++) {
 330                         meanStartPosition += startPosition[i];
 331                         meanEndPosition += endPosition[i];
 332                         meanSeqLength += seqLength[i];
 333                         meanAmbigBases += ambigBases[i];
 334                         meanLongHomoPolymer += longHomoPolymer[i];
 335                 }
 336                 //this is an int divide so the remainder is lost
 337                 meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
 338
 339                 int ptile0_25   = int(size * 0.025);
 340                 int ptile25             = int(size * 0.250);
 341                 int ptile50             = int(size * 0.500);
 342                 int ptile75             = int(size * 0.750);
 343                 int ptile97_5   = int(size * 0.975);
 344                 int ptile100    = size - 1;
 345
 346                 //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
 347                 if (startPosition[0] == -1) {  startPosition[0] = 0;    }
 348                 if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
 349
 350                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 351
 352                 m->mothurOutEndLine();
 353                 m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine();
 354                 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();
 355                 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();
 356                 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();
 357                 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();
 358                 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();
 359                 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();
 360                 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();
 361                 m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
 362
 363                 if (namefile == "") {  m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
 364                 else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
 365
 366                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 367
 368                 m->mothurOutEndLine();
 369                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 370                 m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
 371                 m->mothurOutEndLine();
 372
 373                 #ifdef USE_MPI
 374                         }
 375                 #endif
 376
 377                 return 0;
 378         }
 379         catch(exception& e) {
 380                 m->errorOut(e, "SeqSummaryCommand", "execute");
 381                 exit(1);
 382         }
 383 }
 384 /**************************************************************************************/
 385 int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
 386         try {
 387
 388                 ofstream outSummary;
 389                 m->openOutputFile(sumFile, outSummary);
 390
 391                 //print header if you are process 0
 392                 if (filePos->start == 0) {
 393                         outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
 394                 }
 395
 396                 ifstream in;
 397                 m->openInputFile(filename, in);
 398
 399                 in.seekg(filePos->start);
 400
 401                 bool done = false;
 402                 int count = 0;
 403
 404                 while (!done) {
 405
 406                         if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
 407
 408                         Sequence current(in); m->gobble(in);
 409
 410                         if (current.getName() != "") {
 411
 412                                 int num = 1;
 413                                 if (namefile != "") {
 414                                         //make sure this sequence is in the namefile, else error
 415                                         map<string, int>::iterator it = nameMap.find(current.getName());
 416
 417                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 418                                         else { num = it->second; }
 419                                 }
 420
 421                                 //for each sequence this sequence represents
 422                                 for (int i = 0; i < num; i++) {
 423                                         startPosition.push_back(current.getStartPos());
 424                                         endPosition.push_back(current.getEndPos());
 425                                         seqLength.push_back(current.getNumBases());
 426                                         ambigBases.push_back(current.getAmbigBases());
 427                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 428                                 }
 429
 430                                 count++;
 431                                 outSummary << current.getName() << '\t';
 432                                 outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
 433                                 outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
 434                                 outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
 435                         }
 436
 437                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 438                                 unsigned long long pos = in.tellg();
 439                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 440                         #else
 441                                 if (in.eof()) { break; }
 442                         #endif
 443
 444                         //report progress
 445                         //if((count) % 100 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 446                 }
 447                 //report progress
 448                 //if((count) % 100 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 449
 450                 in.close();
 451
 452                 return count;
 453         }
 454         catch(exception& e) {
 455                 m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
 456                 exit(1);
 457         }
 458 }
 459 #ifdef USE_MPI
 460 /**************************************************************************************/
 461 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) {
 462         try {
 463
 464                 int pid;
 465                 MPI_Status status;
 466                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 467
 468                 for(int i=0;i<num;i++){
 469
 470                         if (m->control_pressed) { return 0; }
 471
 472                         //read next sequence
 473                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 474
 475                         char* buf4 = new char[length];
 476                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 477
 478                         string tempBuf = buf4;
 479                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 480                         istringstream iss (tempBuf,istringstream::in);
 481                         delete buf4;
 482
 483                         Sequence current(iss);
 484
 485                         if (current.getName() != "") {
 486
 487                                 int num = 1;
 488                                 if (namefile != "") {
 489                                         //make sure this sequence is in the namefile, else error
 490                                         map<string, int>::iterator it = nameMap.find(current.getName());
 491
 492                                         if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; }
 493                                         else { num = it->second; }
 494                                 }
 495
 496                                 //for each sequence this sequence represents
 497                                 for (int i = 0; i < num; i++) {
 498                                         startPosition.push_back(current.getStartPos());
 499                                         endPosition.push_back(current.getEndPos());
 500                                         seqLength.push_back(current.getNumBases());
 501                                         ambigBases.push_back(current.getAmbigBases());
 502                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 503                                 }
 504
 505                                 string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
 506                                 outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n";
 507
 508                                 //output to file
 509                                 length = outputString.length();
 510                                 char* buf3 = new char[length];
 511                                 memcpy(buf3, outputString.c_str(), length);
 512
 513                                 MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
 514                                 delete buf3;
 515                         }
 516                 }
 517
 518                 return 0;
 519         }
 520         catch(exception& e) {
 521                 m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
 522                 exit(1);
 523         }
 524 }
 525 #endif
 526 /**************************************************************************************************/
 527 int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
 528         try {
 529                 int process = 1;
 530                 int num = 0;
 531                 processIDS.clear();
 532
 533 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 534
 535                 //loop through and create all the processes you want
 536                 while (process != processors) {
 537                         int pid = fork();
 538
 539                         if (pid > 0) {
 540                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 541                                 process++;
 542                         }else if (pid == 0){
 543                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
 544
 545                                 //pass numSeqs to parent
 546                                 ofstream out;
 547                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 548                                 m->openOutputFile(tempFile, out);
 549
 550                                 out << num << endl;
 551                                 out << startPosition.size() << endl;
 552                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 553                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 554                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 555                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 556                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 557
 558                                 out.close();
 559
 560                                 exit(0);
 561                         }else {
 562                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 563                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 564                                 exit(0);
 565                         }
 566                 }
 567
 568                 //do your part
 569                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile, lines[0]);
 570
 571                 //force parent to wait until all the processes are done
 572                 for (int i=0;i<processIDS.size();i++) {
 573                         int temp = processIDS[i];
 574                         wait(&temp);
 575                 }
 576
 577                 //parent reads in and combine Filter info
 578                 for (int i = 0; i < processIDS.size(); i++) {
 579                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 580                         ifstream in;
 581                         m->openInputFile(tempFilename, in);
 582
 583                         int temp, tempNum;
 584                         in >> tempNum; m->gobble(in); num += tempNum;
 585                         in >> tempNum; m->gobble(in);
 586                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 587                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 588                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 589                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 590                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 591
 592                         in.close();
 593                         m->mothurRemove(tempFilename);
 594
 595                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 596                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 597                 }
 598
 599 #else
 600                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 601                 //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
 602                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 603                 //Taking advantage of shared memory to allow both threads to add info to vectors.
 604                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 605
 606                 vector<seqSumData*> pDataArray;
 607                 DWORD   dwThreadIdArray[processors-1];
 608                 HANDLE  hThreadArray[processors-1];
 609
 610                 //Create processor worker threads.
 611                 for( int i=0; i<processors-1; i++ ){
 612
 613             string extension = "";
 614             if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 615                         // Allocate memory for thread data.
 616                         seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, namefile, nameMap);
 617                         pDataArray.push_back(tempSum);
 618
 619                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 620                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 621                         hThreadArray[i] = CreateThread(NULL, 0, MySeqSumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 622                 }
 623
 624         //do your part
 625                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, (sumFile+toString(processors-1)+".temp"), lines[processors-1]);
 626         processIDS.push_back(processors-1);
 627
 628                 //Wait until all threads have terminated.
 629                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 630
 631                 //Close all thread handles and free memory allocations.
 632                 for(int i=0; i < pDataArray.size(); i++){
 633                         num += pDataArray[i]->count;
 634             for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {     startPosition.push_back(pDataArray[i]->startPosition[k]);       }
 635                         for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {   endPosition.push_back(pDataArray[i]->endPosition[k]);       }
 636             for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]);       }
 637             for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) {        ambigBases.push_back(pDataArray[i]->ambigBases[k]);       }
 638             for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) {   longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]);       }
 639                         CloseHandle(hThreadArray[i]);
 640                         delete pDataArray[i];
 641                 }
 642
 643                 //append files
 644                 for(int i=0;i<processIDS.size();i++){
 645                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 646                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 647                 }
 648 #endif
 649                 return num;
 650         }
 651         catch(exception& e) {
 652                 m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
 653                 exit(1);
 654         }
 655 }
 656 /**********************************************************************************************************************/
 657
 658
 659