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 string SeqSummaryCommand::getOutputFileNameTag(string type, string inputName=""){
  50         try {
  51         string outputFileName = "";
  52                 map<string, vector<string> >::iterator it;
  53
  54         //is this a type this command creates
  55         it = outputTypes.find(type);
  56         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  57         else {
  58             if (type == "summary")            {   outputFileName =  "summary";   }
  59             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  60         }
  61         return outputFileName;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "SeqSummaryCommand", "getOutputFileNameTag");
  65                 exit(1);
  66         }
  67 }
  68
  69 //**********************************************************************************************************************
  70 SeqSummaryCommand::SeqSummaryCommand(){
  71         try {
  72                 abort = true; calledHelp = true;
  73                 setParameters();
  74                 vector<string> tempOutNames;
  75                 outputTypes["summary"] = tempOutNames;
  76         }
  77         catch(exception& e) {
  78                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
  79                 exit(1);
  80         }
  81 }
  82 //***************************************************************************************************************
  83
  84 SeqSummaryCommand::SeqSummaryCommand(string option)  {
  85         try {
  86                 abort = false; calledHelp = false;
  87
  88                 //allow user to run help
  89                 if(option == "help") { help(); abort = true; calledHelp = true; }
  90                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  91
  92                 else {
  93                         vector<string> myArray = setParameters();
  94
  95                         OptionParser parser(option);
  96                         map<string,string> parameters = parser.getParameters();
  97
  98                         ValidParameters validParameter("summary.seqs");
  99                         map<string,string>::iterator it;
 100
 101                         //check to make sure all parameters are valid for command
 102                         for (it = parameters.begin(); it != parameters.end(); it++) {
 103                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 104                         }
 105
 106                         //if the user changes the input directory command factory will send this info to us in the output parameter
 107                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 108                         if (inputDir == "not found"){   inputDir = "";          }
 109                         else {
 110                                 string path;
 111                                 it = parameters.find("fasta");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 117                                 }
 118
 119                                 it = parameters.find("name");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 125                                 }
 126                         }
 127
 128                         //initialize outputTypes
 129                         vector<string> tempOutNames;
 130                         outputTypes["summary"] = tempOutNames;
 131
 132                         //check for required parameters
 133                         fastafile = validParameter.validFile(parameters, "fasta", true);
 134                         if (fastafile == "not open") { abort = true; }
 135                         else if (fastafile == "not found") {
 136                                 fastafile = m->getFastaFile();
 137                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 138                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 139                         }else { m->setFastaFile(fastafile); }
 140
 141                         namefile = validParameter.validFile(parameters, "name", true);
 142                         if (namefile == "not open") { namefile = ""; abort = true; }
 143                         else if (namefile == "not found") { namefile = "";  }
 144                         else { m->setNameFile(namefile); }
 145
 146                         //if the user changes the output directory command factory will send this info to us in the output parameter
 147                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 148                                 outputDir = "";
 149                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 150                         }
 151
 152                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 153                         m->setProcessors(temp);
 154                         m->mothurConvert(temp, processors);
 155
 156                         if (namefile == "") {
 157                                 vector<string> files; files.push_back(fastafile);
 158                                 parser.getNameFile(files);
 159                         }
 160
 161                 }
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
 165                 exit(1);
 166         }
 167 }
 168 //***************************************************************************************************************
 169
 170 int SeqSummaryCommand::execute(){
 171         try{
 172
 173                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 174
 175                 //set current fasta to fastafile
 176                 m->setFastaFile(fastafile);
 177
 178                 string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
 179
 180                 int numSeqs = 0;
 181
 182                 vector<int> startPosition;
 183                 vector<int> endPosition;
 184                 vector<int> seqLength;
 185                 vector<int> ambigBases;
 186                 vector<int> longHomoPolymer;
 187
 188                 if (namefile != "") { nameMap = m->readNames(namefile); }
 189
 190                 if (m->control_pressed) { return 0; }
 191
 192 #ifdef USE_MPI
 193                                 int pid, numSeqsPerProcessor;
 194                                 int tag = 2001;
 195                                 int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
 196                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 197                                 vector<unsigned long long> MPIPos;
 198
 199                                 MPI_Status status;
 200                                 MPI_Status statusOut;
 201                                 MPI_File inMPI;
 202                                 MPI_File outMPI;
 203                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 204                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 205
 206                                 char tempFileName[1024];
 207                                 strcpy(tempFileName, fastafile.c_str());
 208
 209                                 char sumFileName[1024];
 210                                 strcpy(sumFileName, summaryFile.c_str());
 211
 212                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 213                                 MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI);
 214
 215                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); return 0;  }
 216
 217                                 if (pid == 0) { //you are the root process
 218                                                 //print header
 219                                                 string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs\n";
 220                                                 int length = outputString.length();
 221                                                 char* buf2 = new char[length];
 222                                                 memcpy(buf2, outputString.c_str(), length);
 223
 224                                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
 225                                                 delete buf2;
 226
 227                                                 MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 228
 229                                                 for(int i = 1; i < processors; i++) {
 230                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 231                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 232                                                 }
 233
 234                                                 //figure out how many sequences you have to do
 235                                                 numSeqsPerProcessor = numSeqs / processors;
 236                                                 int startIndex =  pid * numSeqsPerProcessor;
 237                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 238
 239                                                 //do your part
 240                                                 MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 241
 242                                 }else { //i am the child process
 243
 244                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 245                                         MPIPos.resize(numSeqs+1);
 246                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 247
 248                                         //figure out how many sequences you have to align
 249                                         numSeqsPerProcessor = numSeqs / processors;
 250                                         int startIndex =  pid * numSeqsPerProcessor;
 251                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 252
 253                                         //do your part
 254                                         MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 255                                 }
 256
 257                                 MPI_File_close(&inMPI);
 258                                 MPI_File_close(&outMPI);
 259                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 260
 261                                 if (pid == 0) {
 262                                         //get the info from the child processes
 263                                         for(int i = 1; i < processors; i++) {
 264                                                 int size;
 265                                                 MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 266
 267                                                 vector<int> temp; temp.resize(size+1);
 268
 269                                                 for(int j = 0; j < 5; j++) {
 270
 271                                                         MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 272                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
 273
 274                                                         if (receiveTag == startTag) {
 275                                                                 for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
 276                                                         }else if (receiveTag == endTag) {
 277                                                                 for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
 278                                                         }else if (receiveTag == lengthTag) {
 279                                                                 for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
 280                                                         }else if (receiveTag == baseTag) {
 281                                                                 for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
 282                                                         }else if (receiveTag == lhomoTag) {
 283                                                                 for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
 284                                                         }
 285                                                 }
 286                                         }
 287
 288                                 }else{
 289
 290                                         //send my counts
 291                                         int size = startPosition.size();
 292                                         MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 293
 294                                         startPosition.push_back(startTag);
 295                                         int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 296                                         endPosition.push_back(endTag);
 297                                         ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 298                                         seqLength.push_back(lengthTag);
 299                                         ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 300                                         ambigBases.push_back(baseTag);
 301                                         ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 302                                         longHomoPolymer.push_back(lhomoTag);
 303                                         ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 304                                 }
 305
 306                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 307 #else
 308                         vector<unsigned long long> positions;
 309                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 310                                 positions = m->divideFile(fastafile, processors);
 311                                 for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 312                         #else
 313                                 positions = m->setFilePosFasta(fastafile, numSeqs);
 314                 if (positions.size() < processors) { processors = positions.size(); }
 315
 316                                 //figure out how many sequences you have to process
 317                                 int numSeqsPerProcessor = numSeqs / processors;
 318                                 for (int i = 0; i < processors; i++) {
 319                                         int startIndex =  i * numSeqsPerProcessor;
 320                                         if(i == (processors - 1)){      numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 321                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 322                                 }
 323                         #endif
 324
 325
 326                         if(processors == 1){
 327                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 328                         }else{
 329                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
 330                         }
 331
 332                         if (m->control_pressed) {  return 0; }
 333 #endif
 334
 335                 #ifdef USE_MPI
 336                         if (pid == 0) {
 337                 #endif
 338
 339                 sort(startPosition.begin(), startPosition.end());
 340                 sort(endPosition.begin(), endPosition.end());
 341                 sort(seqLength.begin(), seqLength.end());
 342                 sort(ambigBases.begin(), ambigBases.end());
 343                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 344                 int size = startPosition.size();
 345
 346                 //find means
 347                 float meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
 348                 meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
 349                 for (int i = 0; i < size; i++) {
 350                         meanStartPosition += startPosition[i];
 351                         meanEndPosition += endPosition[i];
 352                         meanSeqLength += seqLength[i];
 353                         meanAmbigBases += ambigBases[i];
 354                         meanLongHomoPolymer += longHomoPolymer[i];
 355                 }
 356                 //this is an int divide so the remainder is lost
 357                 meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
 358
 359                 int ptile0_25   = int(size * 0.025);
 360                 int ptile25             = int(size * 0.250);
 361                 int ptile50             = int(size * 0.500);
 362                 int ptile75             = int(size * 0.750);
 363                 int ptile97_5   = int(size * 0.975);
 364                 int ptile100    = size - 1;
 365
 366                 //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
 367                 if (startPosition[0] == -1) {  startPosition[0] = 0;    }
 368                 if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
 369
 370                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 371
 372                 m->mothurOutEndLine();
 373                 m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine();
 374                 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();
 375                 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();
 376                 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();
 377                 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();
 378                 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();
 379                 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();
 380                 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();
 381                 m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
 382
 383                 if (namefile == "") {  m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
 384                 else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
 385
 386                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 387
 388                 m->mothurOutEndLine();
 389                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 390                 m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
 391                 m->mothurOutEndLine();
 392
 393                 #ifdef USE_MPI
 394                         }
 395                 #endif
 396
 397                 return 0;
 398         }
 399         catch(exception& e) {
 400                 m->errorOut(e, "SeqSummaryCommand", "execute");
 401                 exit(1);
 402         }
 403 }
 404 /**************************************************************************************/
 405 int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
 406         try {
 407
 408                 ofstream outSummary;
 409                 m->openOutputFile(sumFile, outSummary);
 410
 411                 //print header if you are process 0
 412                 if (filePos->start == 0) {
 413                         outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
 414                 }
 415
 416                 ifstream in;
 417                 m->openInputFile(filename, in);
 418
 419                 in.seekg(filePos->start);
 420
 421                 bool done = false;
 422                 int count = 0;
 423
 424                 while (!done) {
 425
 426                         if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
 427
 428                         Sequence current(in); m->gobble(in);
 429
 430                         if (current.getName() != "") {
 431
 432                                 int num = 1;
 433                                 if (namefile != "") {
 434                                         //make sure this sequence is in the namefile, else error
 435                                         map<string, int>::iterator it = nameMap.find(current.getName());
 436
 437                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 438                                         else { num = it->second; }
 439                                 }
 440
 441                                 //for each sequence this sequence represents
 442                                 for (int i = 0; i < num; i++) {
 443                                         startPosition.push_back(current.getStartPos());
 444                                         endPosition.push_back(current.getEndPos());
 445                                         seqLength.push_back(current.getNumBases());
 446                                         ambigBases.push_back(current.getAmbigBases());
 447                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 448                                 }
 449
 450                                 count++;
 451                                 outSummary << current.getName() << '\t';
 452                                 outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
 453                                 outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
 454                                 outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
 455                         }
 456
 457                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 458                                 unsigned long long pos = in.tellg();
 459                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 460                         #else
 461                                 if (in.eof()) { break; }
 462                         #endif
 463
 464                         //report progress
 465                         //if((count) % 100 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 466                 }
 467                 //report progress
 468                 //if((count) % 100 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 469
 470                 in.close();
 471
 472                 return count;
 473         }
 474         catch(exception& e) {
 475                 m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
 476                 exit(1);
 477         }
 478 }
 479 #ifdef USE_MPI
 480 /**************************************************************************************/
 481 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) {
 482         try {
 483
 484                 int pid;
 485                 MPI_Status status;
 486                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 487
 488                 for(int i=0;i<num;i++){
 489
 490                         if (m->control_pressed) { return 0; }
 491
 492                         //read next sequence
 493                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 494
 495                         char* buf4 = new char[length];
 496                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 497
 498                         string tempBuf = buf4;
 499                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 500                         istringstream iss (tempBuf,istringstream::in);
 501                         delete buf4;
 502
 503                         Sequence current(iss);
 504
 505                         if (current.getName() != "") {
 506
 507                                 int num = 1;
 508                                 if (namefile != "") {
 509                                         //make sure this sequence is in the namefile, else error
 510                                         map<string, int>::iterator it = nameMap.find(current.getName());
 511
 512                                         if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; }
 513                                         else { num = it->second; }
 514                                 }
 515
 516                                 //for each sequence this sequence represents
 517                                 for (int i = 0; i < num; i++) {
 518                                         startPosition.push_back(current.getStartPos());
 519                                         endPosition.push_back(current.getEndPos());
 520                                         seqLength.push_back(current.getNumBases());
 521                                         ambigBases.push_back(current.getAmbigBases());
 522                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 523                                 }
 524
 525                                 string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
 526                                 outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n";
 527
 528                                 //output to file
 529                                 length = outputString.length();
 530                                 char* buf3 = new char[length];
 531                                 memcpy(buf3, outputString.c_str(), length);
 532
 533                                 MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
 534                                 delete buf3;
 535                         }
 536                 }
 537
 538                 return 0;
 539         }
 540         catch(exception& e) {
 541                 m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
 542                 exit(1);
 543         }
 544 }
 545 #endif
 546 /**************************************************************************************************/
 547 int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
 548         try {
 549                 int process = 1;
 550                 int num = 0;
 551                 processIDS.clear();
 552
 553 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 554
 555                 //loop through and create all the processes you want
 556                 while (process != processors) {
 557                         int pid = fork();
 558
 559                         if (pid > 0) {
 560                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 561                                 process++;
 562                         }else if (pid == 0){
 563                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
 564
 565                                 //pass numSeqs to parent
 566                                 ofstream out;
 567                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 568                                 m->openOutputFile(tempFile, out);
 569
 570                                 out << num << endl;
 571                                 out << startPosition.size() << endl;
 572                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 573                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 574                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 575                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 576                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 577
 578                                 out.close();
 579
 580                                 exit(0);
 581                         }else {
 582                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 583                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 584                                 exit(0);
 585                         }
 586                 }
 587
 588                 //do your part
 589                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile, lines[0]);
 590
 591                 //force parent to wait until all the processes are done
 592                 for (int i=0;i<processIDS.size();i++) {
 593                         int temp = processIDS[i];
 594                         wait(&temp);
 595                 }
 596
 597                 //parent reads in and combine Filter info
 598                 for (int i = 0; i < processIDS.size(); i++) {
 599                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 600                         ifstream in;
 601                         m->openInputFile(tempFilename, in);
 602
 603                         int temp, tempNum;
 604                         in >> tempNum; m->gobble(in); num += tempNum;
 605                         in >> tempNum; m->gobble(in);
 606                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 607                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 608                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 609                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 610                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 611
 612                         in.close();
 613                         m->mothurRemove(tempFilename);
 614
 615                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 616                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 617                 }
 618
 619 #else
 620                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 621                 //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
 622                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 623                 //Taking advantage of shared memory to allow both threads to add info to vectors.
 624                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 625
 626                 vector<seqSumData*> pDataArray;
 627                 DWORD   dwThreadIdArray[processors-1];
 628                 HANDLE  hThreadArray[processors-1];
 629
 630                 //Create processor worker threads.
 631                 for( int i=0; i<processors-1; i++ ){
 632
 633             string extension = "";
 634             if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 635                         // Allocate memory for thread data.
 636                         seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, namefile, nameMap);
 637                         pDataArray.push_back(tempSum);
 638
 639                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 640                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 641                         hThreadArray[i] = CreateThread(NULL, 0, MySeqSumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 642                 }
 643
 644         //do your part
 645                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, (sumFile+toString(processors-1)+".temp"), lines[processors-1]);
 646         processIDS.push_back(processors-1);
 647
 648                 //Wait until all threads have terminated.
 649                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 650
 651                 //Close all thread handles and free memory allocations.
 652                 for(int i=0; i < pDataArray.size(); i++){
 653                         num += pDataArray[i]->count;
 654             for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {     startPosition.push_back(pDataArray[i]->startPosition[k]);       }
 655                         for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {   endPosition.push_back(pDataArray[i]->endPosition[k]);       }
 656             for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]);       }
 657             for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) {        ambigBases.push_back(pDataArray[i]->ambigBases[k]);       }
 658             for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) {   longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]);       }
 659                         CloseHandle(hThreadArray[i]);
 660                         delete pDataArray[i];
 661                 }
 662
 663                 //append files
 664                 for(int i=0;i<processIDS.size();i++){
 665                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 666                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 667                 }
 668 #endif
 669                 return num;
 670         }
 671         catch(exception& e) {
 672                 m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
 673                 exit(1);
 674         }
 675 }
 676 /**********************************************************************************************************************/
 677
 678
 679