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