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","summary",false,true,true); parameters.push_back(pfasta);
  17                 CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
  18         CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
  19                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); 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::getOutputPattern(string type) {
  52     try {
  53         string pattern = "";
  54
  55         if (type == "summary") {  pattern = "[filename],summary"; }
  56         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  57
  58         return pattern;
  59     }
  60     catch(exception& e) {
  61         m->errorOut(e, "SeqSummaryCommand", "getOutputPattern");
  62         exit(1);
  63     }
  64 }
  65
  66 //**********************************************************************************************************************
  67 SeqSummaryCommand::SeqSummaryCommand(){
  68         try {
  69                 abort = true; calledHelp = true;
  70                 setParameters();
  71                 vector<string> tempOutNames;
  72                 outputTypes["summary"] = tempOutNames;
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
  76                 exit(1);
  77         }
  78 }
  79 //***************************************************************************************************************
  80
  81 SeqSummaryCommand::SeqSummaryCommand(string option)  {
  82         try {
  83                 abort = false; calledHelp = false;
  84
  85                 //allow user to run help
  86                 if(option == "help") { help(); abort = true; calledHelp = true; }
  87                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  88
  89                 else {
  90                         vector<string> myArray = setParameters();
  91
  92                         OptionParser parser(option);
  93                         map<string,string> parameters = parser.getParameters();
  94
  95                         ValidParameters validParameter("summary.seqs");
  96                         map<string,string>::iterator it;
  97
  98                         //check to make sure all parameters are valid for command
  99                         for (it = parameters.begin(); it != parameters.end(); it++) {
 100                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 101                         }
 102
 103                         //if the user changes the input directory command factory will send this info to us in the output parameter
 104                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 105                         if (inputDir == "not found"){   inputDir = "";          }
 106                         else {
 107                                 string path;
 108                                 it = parameters.find("fasta");
 109                                 //user has given a template file
 110                                 if(it != parameters.end()){
 111                                         path = m->hasPath(it->second);
 112                                         //if the user has not given a path then, add inputdir. else leave path alone.
 113                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 114                                 }
 115
 116                                 it = parameters.find("name");
 117                                 //user has given a template file
 118                                 if(it != parameters.end()){
 119                                         path = m->hasPath(it->second);
 120                                         //if the user has not given a path then, add inputdir. else leave path alone.
 121                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 122                                 }
 123
 124                 it = parameters.find("count");
 125                                 //user has given a template file
 126                                 if(it != parameters.end()){
 127                                         path = m->hasPath(it->second);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 130                                 }
 131                         }
 132
 133                         //initialize outputTypes
 134                         vector<string> tempOutNames;
 135                         outputTypes["summary"] = tempOutNames;
 136
 137                         //check for required parameters
 138                         fastafile = validParameter.validFile(parameters, "fasta", true);
 139                         if (fastafile == "not open") { abort = true; }
 140                         else if (fastafile == "not found") {
 141                                 fastafile = m->getFastaFile();
 142                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 143                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 144                         }else { m->setFastaFile(fastafile); }
 145
 146                         namefile = validParameter.validFile(parameters, "name", true);
 147                         if (namefile == "not open") { namefile = ""; abort = true; }
 148                         else if (namefile == "not found") { namefile = "";  }
 149                         else { m->setNameFile(namefile); }
 150
 151             countfile = validParameter.validFile(parameters, "count", true);
 152                         if (countfile == "not open") { abort = true; countfile = ""; }
 153                         else if (countfile == "not found") { countfile = ""; }
 154                         else { m->setCountTableFile(countfile); }
 155
 156             if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 157
 158                         //if the user changes the output directory command factory will send this info to us in the output parameter
 159                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 160                                 outputDir = "";
 161                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 162                         }
 163
 164                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 165                         m->setProcessors(temp);
 166                         m->mothurConvert(temp, processors);
 167
 168             if (countfile == "") {
 169                 if (namefile == "") {
 170                     vector<string> files; files.push_back(fastafile);
 171                     parser.getNameFile(files);
 172                 }
 173             }
 174                 }
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
 178                 exit(1);
 179         }
 180 }
 181 //***************************************************************************************************************
 182
 183 int SeqSummaryCommand::execute(){
 184         try{
 185
 186                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 187
 188                 //set current fasta to fastafile
 189                 m->setFastaFile(fastafile);
 190
 191         map<string, string> variables;
 192                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
 193                 string summaryFile = getOutputFileName("summary",variables);
 194
 195                 int numSeqs = 0;
 196
 197                 vector<int> startPosition;
 198                 vector<int> endPosition;
 199                 vector<int> seqLength;
 200                 vector<int> ambigBases;
 201                 vector<int> longHomoPolymer;
 202
 203                 if (namefile != "") { nameMap = m->readNames(namefile); }
 204         else if (countfile != "") {
 205             CountTable ct;
 206             ct.readTable(countfile);
 207             nameMap = ct.getNameMap();
 208         }
 209
 210                 if (m->control_pressed) { return 0; }
 211
 212 #ifdef USE_MPI
 213                                 int pid, numSeqsPerProcessor;
 214                                 int tag = 2001;
 215                                 int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
 216                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 217                                 vector<unsigned long long> MPIPos;
 218
 219                                 MPI_Status status;
 220                                 MPI_Status statusOut;
 221                                 MPI_File inMPI;
 222                                 MPI_File outMPI;
 223                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 224                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 225
 226                                 char tempFileName[1024];
 227                                 strcpy(tempFileName, fastafile.c_str());
 228
 229                                 char sumFileName[1024];
 230                                 strcpy(sumFileName, summaryFile.c_str());
 231
 232                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 233                                 MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI);
 234
 235                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); return 0;  }
 236
 237                                 if (pid == 0) { //you are the root process
 238                                                 //print header
 239                                                 string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs\n";
 240                                                 int length = outputString.length();
 241                                                 char* buf2 = new char[length];
 242                                                 memcpy(buf2, outputString.c_str(), length);
 243
 244                                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
 245                                                 delete buf2;
 246
 247                                                 MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 248
 249                                                 for(int i = 1; i < processors; i++) {
 250                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 251                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 252                                                 }
 253
 254                                                 //figure out how many sequences you have to do
 255                                                 numSeqsPerProcessor = numSeqs / processors;
 256                                                 int startIndex =  pid * numSeqsPerProcessor;
 257                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 258
 259                                                 //do your part
 260                                                 MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 261
 262                                 }else { //i am the child process
 263
 264                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 265                                         MPIPos.resize(numSeqs+1);
 266                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 267
 268                                         //figure out how many sequences you have to align
 269                                         numSeqsPerProcessor = numSeqs / processors;
 270                                         int startIndex =  pid * numSeqsPerProcessor;
 271                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 272
 273                                         //do your part
 274                                         MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 275                                 }
 276
 277                                 MPI_File_close(&inMPI);
 278                                 MPI_File_close(&outMPI);
 279                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 280
 281                                 if (pid == 0) {
 282                                         //get the info from the child processes
 283                                         for(int i = 1; i < processors; i++) {
 284                                                 int size;
 285                                                 MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 286
 287                                                 vector<int> temp; temp.resize(size+1);
 288
 289                                                 for(int j = 0; j < 5; j++) {
 290
 291                                                         MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 292                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
 293
 294                                                         if (receiveTag == startTag) {
 295                                                                 for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
 296                                                         }else if (receiveTag == endTag) {
 297                                                                 for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
 298                                                         }else if (receiveTag == lengthTag) {
 299                                                                 for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
 300                                                         }else if (receiveTag == baseTag) {
 301                                                                 for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
 302                                                         }else if (receiveTag == lhomoTag) {
 303                                                                 for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
 304                                                         }
 305                                                 }
 306                                         }
 307
 308                                 }else{
 309
 310                                         //send my counts
 311                                         int size = startPosition.size();
 312                                         MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 313
 314                                         startPosition.push_back(startTag);
 315                                         int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 316                                         endPosition.push_back(endTag);
 317                                         ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 318                                         seqLength.push_back(lengthTag);
 319                                         ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 320                                         ambigBases.push_back(baseTag);
 321                                         ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 322                                         longHomoPolymer.push_back(lhomoTag);
 323                                         ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 324                                 }
 325
 326                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 327 #else
 328                         vector<unsigned long long> positions;
 329                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 330                                 positions = m->divideFile(fastafile, processors);
 331                                 for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 332                         #else
 333                                 positions = m->setFilePosFasta(fastafile, numSeqs);
 334                 if (positions.size() < processors) { processors = positions.size(); }
 335
 336                                 //figure out how many sequences you have to process
 337                                 int numSeqsPerProcessor = numSeqs / processors;
 338                                 for (int i = 0; i < processors; i++) {
 339                                         int startIndex =  i * numSeqsPerProcessor;
 340                                         if(i == (processors - 1)){      numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 341                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 342                                 }
 343                         #endif
 344
 345
 346                         if(processors == 1){
 347                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 348                         }else{
 349                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
 350                         }
 351
 352                         if (m->control_pressed) {  return 0; }
 353 #endif
 354
 355                 #ifdef USE_MPI
 356                         if (pid == 0) {
 357                 #endif
 358
 359                 sort(startPosition.begin(), startPosition.end());
 360                 sort(endPosition.begin(), endPosition.end());
 361                 sort(seqLength.begin(), seqLength.end());
 362                 sort(ambigBases.begin(), ambigBases.end());
 363                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 364                 int size = startPosition.size();
 365
 366                 //find means
 367                 double meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
 368                 meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
 369                 for (int i = 0; i < size; i++) {
 370                         meanStartPosition += startPosition[i];
 371                         meanEndPosition += endPosition[i];
 372                         meanSeqLength += seqLength[i];
 373                         meanAmbigBases += ambigBases[i];
 374                         meanLongHomoPolymer += longHomoPolymer[i];
 375                 }
 376
 377                 //this is an int divide so the remainder is lost
 378                 meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
 379
 380                 int ptile0_25   = int(size * 0.025);
 381                 int ptile25             = int(size * 0.250);
 382                 int ptile50             = int(size * 0.500);
 383                 int ptile75             = int(size * 0.750);
 384                 int ptile97_5   = int(size * 0.975);
 385                 int ptile100    = size - 1;
 386
 387                 //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
 388                 if (startPosition[0] == -1) {  startPosition[0] = 0;    }
 389                 if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
 390
 391                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 392
 393                 m->mothurOutEndLine();
 394                 m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine();
 395                 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();
 396                 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();
 397                 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();
 398                 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();
 399                 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();
 400                 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();
 401                 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();
 402                 m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
 403
 404                 if ((namefile == "") && (countfile == "")) {  m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
 405                 else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
 406
 407                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 408
 409                 m->mothurOutEndLine();
 410                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 411                 m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
 412                 m->mothurOutEndLine();
 413
 414                 #ifdef USE_MPI
 415                         }
 416                 #endif
 417
 418         //set fasta file as new current fastafile
 419                 string current = "";
 420                 itTypes = outputTypes.find("summary");
 421                 if (itTypes != outputTypes.end()) {
 422                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); }
 423                 }
 424
 425                 return 0;
 426         }
 427         catch(exception& e) {
 428                 m->errorOut(e, "SeqSummaryCommand", "execute");
 429                 exit(1);
 430         }
 431 }
 432 /**************************************************************************************/
 433 int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
 434         try {
 435
 436                 ofstream outSummary;
 437                 m->openOutputFile(sumFile, outSummary);
 438
 439                 //print header if you are process 0
 440                 if (filePos->start == 0) {
 441                         outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
 442                 }
 443
 444                 ifstream in;
 445                 m->openInputFile(filename, in);
 446
 447                 in.seekg(filePos->start);
 448
 449                 bool done = false;
 450                 int count = 0;
 451
 452                 while (!done) {
 453
 454                         if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
 455
 456                         Sequence current(in); m->gobble(in);
 457
 458                         if (current.getName() != "") {
 459
 460                                 int num = 1;
 461                                 if ((namefile != "") || (countfile != "")) {
 462                                         //make sure this sequence is in the namefile, else error
 463                                         map<string, int>::iterator it = nameMap.find(current.getName());
 464
 465                                         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; }
 466                                         else { num = it->second; }
 467                                 }
 468
 469                                 //for each sequence this sequence represents
 470                                 for (int i = 0; i < num; i++) {
 471                                         startPosition.push_back(current.getStartPos());
 472                                         endPosition.push_back(current.getEndPos());
 473                                         seqLength.push_back(current.getNumBases());
 474                                         ambigBases.push_back(current.getAmbigBases());
 475                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 476                                 }
 477
 478                                 count++;
 479                                 outSummary << current.getName() << '\t';
 480                                 outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
 481                                 outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
 482                                 outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
 483                         }
 484
 485                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 486                                 unsigned long long pos = in.tellg();
 487                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 488                         #else
 489                                 if (in.eof()) { break; }
 490                         #endif
 491
 492                         //report progress
 493                         //if((count) % 100 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 494                 }
 495                 //report progress
 496                 //if((count) % 100 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 497
 498                 in.close();
 499
 500                 return count;
 501         }
 502         catch(exception& e) {
 503                 m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
 504                 exit(1);
 505         }
 506 }
 507 #ifdef USE_MPI
 508 /**************************************************************************************/
 509 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) {
 510         try {
 511
 512                 int pid;
 513                 MPI_Status status;
 514                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 515
 516                 for(int i=0;i<num;i++){
 517
 518                         if (m->control_pressed) { return 0; }
 519
 520                         //read next sequence
 521                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 522
 523                         char* buf4 = new char[length];
 524                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 525
 526                         string tempBuf = buf4;
 527                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 528                         istringstream iss (tempBuf,istringstream::in);
 529                         delete buf4;
 530
 531                         Sequence current(iss);
 532
 533                         if (current.getName() != "") {
 534
 535                                 int num = 1;
 536                                 if ((namefile != "") || (countfile != "")) {
 537                                         //make sure this sequence is in the namefile, else error
 538                                         map<string, int>::iterator it = nameMap.find(current.getName());
 539
 540                                         if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your name or count file, please correct." << endl; m->control_pressed = true; }
 541                                         else { num = it->second; }
 542                                 }
 543
 544                                 //for each sequence this sequence represents
 545                                 for (int i = 0; i < num; i++) {
 546                                         startPosition.push_back(current.getStartPos());
 547                                         endPosition.push_back(current.getEndPos());
 548                                         seqLength.push_back(current.getNumBases());
 549                                         ambigBases.push_back(current.getAmbigBases());
 550                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 551                                 }
 552
 553                                 string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
 554                                 outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n";
 555
 556                                 //output to file
 557                                 length = outputString.length();
 558                                 char* buf3 = new char[length];
 559                                 memcpy(buf3, outputString.c_str(), length);
 560
 561                                 MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
 562                                 delete buf3;
 563                         }
 564                 }
 565
 566                 return 0;
 567         }
 568         catch(exception& e) {
 569                 m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
 570                 exit(1);
 571         }
 572 }
 573 #endif
 574 /**************************************************************************************************/
 575 int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
 576         try {
 577                 int process = 1;
 578                 int num = 0;
 579                 processIDS.clear();
 580
 581 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 582
 583                 //loop through and create all the processes you want
 584                 while (process != processors) {
 585                         int pid = fork();
 586
 587                         if (pid > 0) {
 588                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 589                                 process++;
 590                         }else if (pid == 0){
 591                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
 592
 593                                 //pass numSeqs to parent
 594                                 ofstream out;
 595                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 596                                 m->openOutputFile(tempFile, out);
 597
 598                                 out << num << endl;
 599                                 out << startPosition.size() << endl;
 600                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 601                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 602                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 603                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 604                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 605
 606                                 out.close();
 607
 608                                 exit(0);
 609                         }else {
 610                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 611                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 612                                 exit(0);
 613                         }
 614                 }
 615
 616                 //do your part
 617                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile, lines[0]);
 618
 619                 //force parent to wait until all the processes are done
 620                 for (int i=0;i<processIDS.size();i++) {
 621                         int temp = processIDS[i];
 622                         wait(&temp);
 623                 }
 624
 625                 //parent reads in and combine Filter info
 626                 for (int i = 0; i < processIDS.size(); i++) {
 627                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 628                         ifstream in;
 629                         m->openInputFile(tempFilename, in);
 630
 631                         int temp, tempNum;
 632                         in >> tempNum; m->gobble(in); num += tempNum;
 633                         in >> tempNum; m->gobble(in);
 634                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 635                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 636                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 637                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 638                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 639
 640                         in.close();
 641                         m->mothurRemove(tempFilename);
 642
 643                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 644                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 645                 }
 646
 647 #else
 648                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 649                 //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
 650                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 651                 //Taking advantage of shared memory to allow both threads to add info to vectors.
 652                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 653
 654                 vector<seqSumData*> pDataArray;
 655                 DWORD   dwThreadIdArray[processors-1];
 656                 HANDLE  hThreadArray[processors-1];
 657
 658                 bool hasNameMap = false;
 659         if ((namefile !="") || (countfile != "")) { hasNameMap = true; }
 660
 661                 //Create processor worker threads.
 662                 for( int i=0; i<processors-1; i++ ){
 663
 664             string extension = "";
 665             if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 666                         // Allocate memory for thread data.
 667                         seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, hasNameMap, nameMap);
 668                         pDataArray.push_back(tempSum);
 669
 670                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 671                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 672                         hThreadArray[i] = CreateThread(NULL, 0, MySeqSumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 673                 }
 674
 675         //do your part
 676                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, (sumFile+toString(processors-1)+".temp"), lines[processors-1]);
 677         processIDS.push_back(processors-1);
 678
 679                 //Wait until all threads have terminated.
 680                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 681
 682                 //Close all thread handles and free memory allocations.
 683                 for(int i=0; i < pDataArray.size(); i++){
 684                         num += pDataArray[i]->count;
 685             if (pDataArray[i]->count != pDataArray[i]->end) {
 686                 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
 687             }
 688             for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {     startPosition.push_back(pDataArray[i]->startPosition[k]);       }
 689                         for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {   endPosition.push_back(pDataArray[i]->endPosition[k]);       }
 690             for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]);       }
 691             for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) {        ambigBases.push_back(pDataArray[i]->ambigBases[k]);       }
 692             for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) {   longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]);       }
 693                         CloseHandle(hThreadArray[i]);
 694                         delete pDataArray[i];
 695                 }
 696
 697                 //append files
 698                 for(int i=0;i<processIDS.size();i++){
 699                         m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
 700                         m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
 701                 }
 702 #endif
 703                 return num;
 704         }
 705         catch(exception& e) {
 706                 m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
 707                 exit(1);
 708         }
 709 }
 710 /**********************************************************************************************************************/
 711
 712
 713