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