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 "counttable.h"
  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", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
  18         CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
  19                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  20                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  21                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  22
  23                 vector<string> myArray;
  24                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  25                 return myArray;
  26         }
  27         catch(exception& e) {
  28                 m->errorOut(e, "SeqSummaryCommand", "setParameters");
  29                 exit(1);
  30         }
  31 }
  32 //**********************************************************************************************************************
  33 string SeqSummaryCommand::getHelpString(){
  34         try {
  35                 string helpString = "";
  36                 helpString += "The summary.seqs command reads a fastafile and summarizes the sequences.\n";
  37                 helpString += "The summary.seqs command parameters are fasta, name, count and processors, fasta is required, unless you have a valid current fasta file.\n";
  38                 helpString += "The name parameter allows you to enter a name file associated with your fasta file. \n";
  39         helpString += "The count parameter allows you to enter a count file associated with your fasta file. \n";
  40                 helpString += "The summary.seqs command should be in the following format: \n";
  41                 helpString += "summary.seqs(fasta=yourFastaFile, processors=2) \n";
  42                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  43                 return helpString;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "SeqSummaryCommand", "getHelpString");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 string SeqSummaryCommand::getOutputFileNameTag(string type, string inputName=""){
  52         try {
  53         string outputFileName = "";
  54                 map<string, vector<string> >::iterator it;
  55
  56         //is this a type this command creates
  57         it = outputTypes.find(type);
  58         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  59         else {
  60             if (type == "summary")            {   outputFileName =  "summary";   }
  61             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  62         }
  63         return outputFileName;
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "SeqSummaryCommand", "getOutputFileNameTag");
  67                 exit(1);
  68         }
  69 }
  70
  71 //**********************************************************************************************************************
  72 SeqSummaryCommand::SeqSummaryCommand(){
  73         try {
  74                 abort = true; calledHelp = true;
  75                 setParameters();
  76                 vector<string> tempOutNames;
  77                 outputTypes["summary"] = tempOutNames;
  78         }
  79         catch(exception& e) {
  80                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
  81                 exit(1);
  82         }
  83 }
  84 //***************************************************************************************************************
  85
  86 SeqSummaryCommand::SeqSummaryCommand(string option)  {
  87         try {
  88                 abort = false; calledHelp = false;
  89
  90                 //allow user to run help
  91                 if(option == "help") { help(); abort = true; calledHelp = true; }
  92                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  93
  94                 else {
  95                         vector<string> myArray = setParameters();
  96
  97                         OptionParser parser(option);
  98                         map<string,string> parameters = parser.getParameters();
  99
 100                         ValidParameters validParameter("summary.seqs");
 101                         map<string,string>::iterator it;
 102
 103                         //check to make sure all parameters are valid for command
 104                         for (it = parameters.begin(); it != parameters.end(); it++) {
 105                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 106                         }
 107
 108                         //if the user changes the input directory command factory will send this info to us in the output parameter
 109                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 110                         if (inputDir == "not found"){   inputDir = "";          }
 111                         else {
 112                                 string path;
 113                                 it = parameters.find("fasta");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 119                                 }
 120
 121                                 it = parameters.find("name");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 127                                 }
 128
 129                 it = parameters.find("count");
 130                                 //user has given a template file
 131                                 if(it != parameters.end()){
 132                                         path = m->hasPath(it->second);
 133                                         //if the user has not given a path then, add inputdir. else leave path alone.
 134                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 135                                 }
 136                         }
 137
 138                         //initialize outputTypes
 139                         vector<string> tempOutNames;
 140                         outputTypes["summary"] = tempOutNames;
 141
 142                         //check for required parameters
 143                         fastafile = validParameter.validFile(parameters, "fasta", true);
 144                         if (fastafile == "not open") { abort = true; }
 145                         else if (fastafile == "not found") {
 146                                 fastafile = m->getFastaFile();
 147                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 148                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 149                         }else { m->setFastaFile(fastafile); }
 150
 151                         namefile = validParameter.validFile(parameters, "name", true);
 152                         if (namefile == "not open") { namefile = ""; abort = true; }
 153                         else if (namefile == "not found") { namefile = "";  }
 154                         else { m->setNameFile(namefile); }
 155
 156             countfile = validParameter.validFile(parameters, "count", true);
 157                         if (countfile == "not open") { abort = true; countfile = ""; }
 158                         else if (countfile == "not found") { countfile = ""; }
 159                         else { m->setCountTableFile(countfile); }
 160
 161             if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 162
 163                         //if the user changes the output directory command factory will send this info to us in the output parameter
 164                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 165                                 outputDir = "";
 166                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 167                         }
 168
 169                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 170                         m->setProcessors(temp);
 171                         m->mothurConvert(temp, processors);
 172
 173             if (countfile == "") {
 174                 if (namefile == "") {
 175                     vector<string> files; files.push_back(fastafile);
 176                     parser.getNameFile(files);
 177                 }
 178             }
 179                 }
 180         }
 181         catch(exception& e) {
 182                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
 183                 exit(1);
 184         }
 185 }
 186 //***************************************************************************************************************
 187
 188 int SeqSummaryCommand::execute(){
 189         try{
 190
 191                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 192
 193                 //set current fasta to fastafile
 194                 m->setFastaFile(fastafile);
 195
 196                 string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
 197
 198                 int numSeqs = 0;
 199
 200                 vector<int> startPosition;
 201                 vector<int> endPosition;
 202                 vector<int> seqLength;
 203                 vector<int> ambigBases;
 204                 vector<int> longHomoPolymer;
 205
 206                 if (namefile != "") { nameMap = m->readNames(namefile); }
 207         else if (countfile != "") {
 208             CountTable ct;
 209             ct.readTable(countfile);
 210             nameMap = ct.getNameMap();
 211         }
 212
 213                 if (m->control_pressed) { return 0; }
 214
 215 #ifdef USE_MPI
 216                                 int pid, numSeqsPerProcessor;
 217                                 int tag = 2001;
 218                                 int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
 219                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 220                                 vector<unsigned long long> MPIPos;
 221
 222                                 MPI_Status status;
 223                                 MPI_Status statusOut;
 224                                 MPI_File inMPI;
 225                                 MPI_File outMPI;
 226                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 227                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 228
 229                                 char tempFileName[1024];
 230                                 strcpy(tempFileName, fastafile.c_str());
 231
 232                                 char sumFileName[1024];
 233                                 strcpy(sumFileName, summaryFile.c_str());
 234
 235                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 236                                 MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI);
 237
 238                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); return 0;  }
 239
 240                                 if (pid == 0) { //you are the root process
 241                                                 //print header
 242                                                 string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs\n";
 243                                                 int length = outputString.length();
 244                                                 char* buf2 = new char[length];
 245                                                 memcpy(buf2, outputString.c_str(), length);
 246
 247                                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
 248                                                 delete buf2;
 249
 250                                                 MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 251
 252                                                 for(int i = 1; i < processors; i++) {
 253                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 254                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 255                                                 }
 256
 257                                                 //figure out how many sequences you have to do
 258                                                 numSeqsPerProcessor = numSeqs / processors;
 259                                                 int startIndex =  pid * numSeqsPerProcessor;
 260                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 261
 262                                                 //do your part
 263                                                 MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 264
 265                                 }else { //i am the child process
 266
 267                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 268                                         MPIPos.resize(numSeqs+1);
 269                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 270
 271                                         //figure out how many sequences you have to align
 272                                         numSeqsPerProcessor = numSeqs / processors;
 273                                         int startIndex =  pid * numSeqsPerProcessor;
 274                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 275
 276                                         //do your part
 277                                         MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 278                                 }
 279
 280                                 MPI_File_close(&inMPI);
 281                                 MPI_File_close(&outMPI);
 282                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 283
 284                                 if (pid == 0) {
 285                                         //get the info from the child processes
 286                                         for(int i = 1; i < processors; i++) {
 287                                                 int size;
 288                                                 MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 289
 290                                                 vector<int> temp; temp.resize(size+1);
 291
 292                                                 for(int j = 0; j < 5; j++) {
 293
 294                                                         MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 295                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
 296
 297                                                         if (receiveTag == startTag) {
 298                                                                 for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
 299                                                         }else if (receiveTag == endTag) {
 300                                                                 for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
 301                                                         }else if (receiveTag == lengthTag) {
 302                                                                 for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
 303                                                         }else if (receiveTag == baseTag) {
 304                                                                 for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
 305                                                         }else if (receiveTag == lhomoTag) {
 306                                                                 for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
 307                                                         }
 308                                                 }
 309                                         }
 310
 311                                 }else{
 312
 313                                         //send my counts
 314                                         int size = startPosition.size();
 315                                         MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 316
 317                                         startPosition.push_back(startTag);
 318                                         int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 319                                         endPosition.push_back(endTag);
 320                                         ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 321                                         seqLength.push_back(lengthTag);
 322                                         ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 323                                         ambigBases.push_back(baseTag);
 324                                         ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 325                                         longHomoPolymer.push_back(lhomoTag);
 326                                         ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 327                                 }
 328
 329                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 330 #else
 331                         vector<unsigned long long> positions;
 332                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 333                                 positions = m->divideFile(fastafile, processors);
 334                                 for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 335                         #else
 336                                 positions = m->setFilePosFasta(fastafile, numSeqs);
 337                 if (positions.size() < processors) { processors = positions.size(); }
 338
 339                                 //figure out how many sequences you have to process
 340                                 int numSeqsPerProcessor = numSeqs / processors;
 341                                 for (int i = 0; i < processors; i++) {
 342                                         int startIndex =  i * numSeqsPerProcessor;
 343                                         if(i == (processors - 1)){      numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 344                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 345                                 }
 346                         #endif
 347
 348
 349                         if(processors == 1){
 350                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 351                         }else{
 352                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
 353                         }
 354
 355                         if (m->control_pressed) {  return 0; }
 356 #endif
 357
 358                 #ifdef USE_MPI
 359                         if (pid == 0) {
 360                 #endif
 361
 362                 sort(startPosition.begin(), startPosition.end());
 363                 sort(endPosition.begin(), endPosition.end());
 364                 sort(seqLength.begin(), seqLength.end());
 365                 sort(ambigBases.begin(), ambigBases.end());
 366                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 367                 int size = startPosition.size();
 368
 369                 //find means
 370                 double meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
 371                 meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
 372                 for (int i = 0; i < size; i++) {
 373                         meanStartPosition += startPosition[i];
 374                         meanEndPosition += endPosition[i];
 375                         meanSeqLength += seqLength[i];
 376                         meanAmbigBases += ambigBases[i];
 377                         meanLongHomoPolymer += longHomoPolymer[i];
 378                 }
 379
 380                 //this is an int divide so the remainder is lost
 381                 meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
 382
 383                 int ptile0_25   = int(size * 0.025);
 384                 int ptile25             = int(size * 0.250);
 385                 int ptile50             = int(size * 0.500);
 386                 int ptile75             = int(size * 0.750);
 387                 int ptile97_5   = int(size * 0.975);
 388                 int ptile100    = size - 1;
 389
 390                 //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
 391                 if (startPosition[0] == -1) {  startPosition[0] = 0;    }
 392                 if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
 393
 394                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 395
 396                 m->mothurOutEndLine();
 397                 m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine();
 398                 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();
 399                 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();
 400                 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();
 401                 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();
 402                 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();
 403                 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();
 404                 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();
 405                 m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
 406
 407                 if ((namefile == "") && (countfile == "")) {  m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
 408                 else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
 409
 410                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 411
 412                 m->mothurOutEndLine();
 413                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 414                 m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
 415                 m->mothurOutEndLine();
 416
 417                 #ifdef USE_MPI
 418                         }
 419                 #endif
 420
 421                 return 0;
 422         }
 423         catch(exception& e) {
 424                 m->errorOut(e, "SeqSummaryCommand", "execute");
 425                 exit(1);
 426         }
 427 }
 428 /**************************************************************************************/
 429 int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
 430         try {
 431
 432                 ofstream outSummary;
 433                 m->openOutputFile(sumFile, outSummary);
 434
 435                 //print header if you are process 0
 436                 if (filePos->start == 0) {
 437                         outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
 438                 }
 439
 440                 ifstream in;
 441                 m->openInputFile(filename, in);
 442
 443                 in.seekg(filePos->start);
 444
 445                 bool done = false;
 446                 int count = 0;
 447
 448                 while (!done) {
 449
 450                         if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
 451
 452                         Sequence current(in); m->gobble(in);
 453
 454                         if (current.getName() != "") {
 455
 456                                 int num = 1;
 457                                 if ((namefile != "") || (countfile != "")) {
 458                                         //make sure this sequence is in the namefile, else error
 459                                         map<string, int>::iterator it = nameMap.find(current.getName());
 460
 461                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your name or count file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 462                                         else { num = it->second; }
 463                                 }
 464
 465                                 //for each sequence this sequence represents
 466                                 for (int i = 0; i < num; i++) {
 467                                         startPosition.push_back(current.getStartPos());
 468                                         endPosition.push_back(current.getEndPos());
 469                                         seqLength.push_back(current.getNumBases());
 470                                         ambigBases.push_back(current.getAmbigBases());
 471                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 472                                 }
 473
 474                                 count++;
 475                                 outSummary << current.getName() << '\t';
 476                                 outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
 477                                 outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
 478                                 outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
 479                         }
 480
 481                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 482                                 unsigned long long pos = in.tellg();
 483                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 484                         #else
 485                                 if (in.eof()) { break; }
 486                         #endif
 487
 488                         //report progress
 489                         //if((count) % 100 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 490                 }
 491                 //report progress
 492                 //if((count) % 100 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 493
 494                 in.close();
 495
 496                 return count;
 497         }
 498         catch(exception& e) {
 499                 m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
 500                 exit(1);
 501         }
 502 }
 503 #ifdef USE_MPI
 504 /**************************************************************************************/
 505 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) {
 506         try {
 507
 508                 int pid;
 509                 MPI_Status status;
 510                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 511
 512                 for(int i=0;i<num;i++){
 513
 514                         if (m->control_pressed) { return 0; }
 515
 516                         //read next sequence
 517                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 518
 519                         char* buf4 = new char[length];
 520                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 521
 522                         string tempBuf = buf4;
 523                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 524                         istringstream iss (tempBuf,istringstream::in);
 525                         delete buf4;
 526
 527                         Sequence current(iss);
 528
 529                         if (current.getName() != "") {
 530
 531                                 int num = 1;
 532                                 if ((namefile != "") || (countfile != "")) {
 533                                         //make sure this sequence is in the namefile, else error
 534                                         map<string, int>::iterator it = nameMap.find(current.getName());
 535
 536                                         if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your name or count file, please correct." << endl; m->control_pressed = true; }
 537                                         else { num = it->second; }
 538                                 }
 539
 540                                 //for each sequence this sequence represents
 541                                 for (int i = 0; i < num; i++) {
 542                                         startPosition.push_back(current.getStartPos());
 543                                         endPosition.push_back(current.getEndPos());
 544                                         seqLength.push_back(current.getNumBases());
 545                                         ambigBases.push_back(current.getAmbigBases());
 546                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 547                                 }
 548
 549                                 string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
 550                                 outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n";
 551
 552                                 //output to file
 553                                 length = outputString.length();
 554                                 char* buf3 = new char[length];
 555                                 memcpy(buf3, outputString.c_str(), length);
 556
 557                                 MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
 558                                 delete buf3;
 559                         }
 560                 }
 561
 562                 return 0;
 563         }
 564         catch(exception& e) {
 565                 m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
 566                 exit(1);
 567         }
 568 }
 569 #endif
 570 /**************************************************************************************************/
 571 int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
 572         try {
 573                 int process = 1;
 574                 int num = 0;
 575                 processIDS.clear();
 576
 577 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 578
 579                 //loop through and create all the processes you want
 580                 while (process != processors) {
 581                         int pid = fork();
 582
 583                         if (pid > 0) {
 584                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 585                                 process++;
 586                         }else if (pid == 0){
 587                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
 588
 589                                 //pass numSeqs to parent
 590                                 ofstream out;
 591                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 592                                 m->openOutputFile(tempFile, out);
 593
 594                                 out << num << endl;
 595                                 out << startPosition.size() << endl;
 596                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 597                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 598                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 599                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 600                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 601
 602                                 out.close();
 603
 604                                 exit(0);
 605                         }else {
 606                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 607                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 608                                 exit(0);
 609                         }
 610                 }
 611
 612                 //do your part
 613                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile, lines[0]);
 614
 615                 //force parent to wait until all the processes are done
 616                 for (int i=0;i<processIDS.size();i++) {
 617                         int temp = processIDS[i];
 618                         wait(&temp);
 619                 }
 620
 621                 //parent reads in and combine Filter info
 622                 for (int i = 0; i < processIDS.size(); i++) {
 623                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 624                         ifstream in;
 625                         m->openInputFile(tempFilename, in);
 626
 627                         int temp, tempNum;
 628                         in >> tempNum; m->gobble(in); num += tempNum;
 629                         in >> tempNum; m->gobble(in);
 630                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 631                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 632                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 633                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 634                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 635
 636                         in.close();
 637                         m->mothurRemove(tempFilename);
 638
 639                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 640                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 641                 }
 642
 643 #else
 644                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 645                 //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
 646                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 647                 //Taking advantage of shared memory to allow both threads to add info to vectors.
 648                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 649
 650                 vector<seqSumData*> pDataArray;
 651                 DWORD   dwThreadIdArray[processors-1];
 652                 HANDLE  hThreadArray[processors-1];
 653
 654                 bool hasNameMap = false;
 655         if ((namefile !="") || (countfile != "")) { hasNameMap = true; }
 656
 657                 //Create processor worker threads.
 658                 for( int i=0; i<processors-1; i++ ){
 659
 660             string extension = "";
 661             if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 662                         // Allocate memory for thread data.
 663                         seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, hasNameMap, nameMap);
 664                         pDataArray.push_back(tempSum);
 665
 666                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 667                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 668                         hThreadArray[i] = CreateThread(NULL, 0, MySeqSumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 669                 }
 670
 671         //do your part
 672                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, (sumFile+toString(processors-1)+".temp"), lines[processors-1]);
 673         processIDS.push_back(processors-1);
 674
 675                 //Wait until all threads have terminated.
 676                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 677
 678                 //Close all thread handles and free memory allocations.
 679                 for(int i=0; i < pDataArray.size(); i++){
 680                         num += pDataArray[i]->count;
 681             for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {     startPosition.push_back(pDataArray[i]->startPosition[k]);       }
 682                         for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {   endPosition.push_back(pDataArray[i]->endPosition[k]);       }
 683             for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]);       }
 684             for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) {        ambigBases.push_back(pDataArray[i]->ambigBases[k]);       }
 685             for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) {   longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]);       }
 686                         CloseHandle(hThreadArray[i]);
 687                         delete pDataArray[i];
 688                 }
 689
 690                 //append files
 691                 for(int i=0;i<processIDS.size();i++){
 692                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 693                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 694                 }
 695 #endif
 696                 return num;
 697         }
 698         catch(exception& e) {
 699                 m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
 700                 exit(1);
 701         }
 702 }
 703 /**********************************************************************************************************************/
 704
 705
 706