summaryqualcommand.cpp

   1 /*
   2  *  summaryqualcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/28/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "summaryqualcommand.h"
  11 #include "counttable.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> SummaryQualCommand::setParameters(){
  15         try {
  16                 CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqual);
  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, "SummaryQualCommand", "setParameters");
  29                 exit(1);
  30         }
  31 }
  32 //**********************************************************************************************************************
  33 string SummaryQualCommand::getHelpString(){
  34         try {
  35                 string helpString = "";
  36                 helpString += "The summary.qual command reads a quality file and an optional name or count file, and summarizes the quality information.\n";
  37                 helpString += "The summary.tax command parameters are qfile, name, count and processors. qfile is required, unless you have a valid current quality file.\n";
  38                 helpString += "The name parameter allows you to enter a name file associated with your quality file. \n";
  39         helpString += "The count parameter allows you to enter a count file associated with your quality file. \n";
  40                 helpString += "The summary.qual command should be in the following format: \n";
  41                 helpString += "summary.qual(qfile=yourQualityFile) \n";
  42                 helpString += "Note: No spaces between parameter labels (i.e. qfile), '=' and parameters (i.e.yourQualityFile).\n";
  43                 return helpString;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "SummaryQualCommand", "getHelpString");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 string SummaryQualCommand::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 =  "qual.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, "SummaryQualCommand", "getOutputFileNameTag");
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71 SummaryQualCommand::SummaryQualCommand(){
  72         try {
  73                 abort = true; calledHelp = true;
  74                 setParameters();
  75                 vector<string> tempOutNames;
  76                 outputTypes["summary"] = tempOutNames;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "SummaryQualCommand", "SummaryQualCommand");
  80                 exit(1);
  81         }
  82 }
  83 //***************************************************************************************************************
  84
  85 SummaryQualCommand::SummaryQualCommand(string option)  {
  86         try {
  87                 abort = false; calledHelp = false;
  88
  89                 //allow user to run help
  90                 if(option == "help") { help(); abort = true; calledHelp = true; }
  91                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  92
  93                 else {
  94                         vector<string> myArray = setParameters();
  95
  96                         OptionParser parser(option);
  97                         map<string,string> parameters = parser.getParameters();
  98
  99                         ValidParameters validParameter;
 100                         map<string,string>::iterator it;
 101
 102                         //check to make sure all parameters are valid for command
 103                         for (it = parameters.begin(); it != parameters.end(); it++) {
 104                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 105                         }
 106
 107                         //if the user changes the input directory command factory will send this info to us in the output parameter
 108                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 109                         if (inputDir == "not found"){   inputDir = "";          }
 110                         else {
 111                                 string path;
 112                                 it = parameters.find("qfile");
 113                                 //user has given a template file
 114                                 if(it != parameters.end()){
 115                                         path = m->hasPath(it->second);
 116                                         //if the user has not given a path then, add inputdir. else leave path alone.
 117                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 118                                 }
 119
 120                                 it = parameters.find("name");
 121                                 //user has given a template file
 122                                 if(it != parameters.end()){
 123                                         path = m->hasPath(it->second);
 124                                         //if the user has not given a path then, add inputdir. else leave path alone.
 125                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 126                                 }
 127
 128                 it = parameters.find("count");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 134                                 }
 135                         }
 136
 137                         //initialize outputTypes
 138                         vector<string> tempOutNames;
 139                         outputTypes["summary"] = tempOutNames;
 140
 141                         //check for required parameters
 142                         qualfile = validParameter.validFile(parameters, "qfile", true);
 143                         if (qualfile == "not open") { qualfile = ""; abort = true; }
 144                         else if (qualfile == "not found") {
 145                                 qualfile = m->getQualFile();
 146                                 if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
 147                                 else {  m->mothurOut("You have no current quality file and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
 148                         }else { m->setQualFile(qualfile); }
 149
 150                         namefile = validParameter.validFile(parameters, "name", true);
 151                         if (namefile == "not open") { namefile = ""; abort = true; }
 152                         else if (namefile == "not found") { namefile = "";  }
 153                         else { m->setNameFile(namefile); }
 154
 155             countfile = validParameter.validFile(parameters, "count", true);
 156                         if (countfile == "not open") { abort = true; countfile = ""; }
 157                         else if (countfile == "not found") { countfile = ""; }
 158                         else { m->setCountTableFile(countfile); }
 159
 160             if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 161
 162                         //if the user changes the output directory command factory will send this info to us in the output parameter
 163                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 164                                 outputDir = "";
 165                                 outputDir += m->hasPath(qualfile); //if user entered a file with a path then preserve it
 166                         }
 167
 168                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 169                         m->setProcessors(temp);
 170                         m->mothurConvert(temp, processors);
 171
 172
 173                         if (countfile == "") {
 174                 if (namefile == "") {
 175                     vector<string> files; files.push_back(qualfile);
 176                     parser.getNameFile(files);
 177                 }
 178             }
 179                 }
 180         }
 181         catch(exception& e) {
 182                 m->errorOut(e, "SummaryQualCommand", "SummaryQualCommand");
 183                 exit(1);
 184         }
 185 }
 186 //***************************************************************************************************************
 187 int SummaryQualCommand::execute(){
 188         try{
 189
 190                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 191
 192                 int start = time(NULL);
 193                 int numSeqs = 0;
 194
 195                 vector<int> position;
 196                 vector<int> averageQ;
 197                 vector< vector<int> > scores;
 198
 199                 if (m->control_pressed) { return 0; }
 200
 201                 if (namefile != "") { nameMap = m->readNames(namefile); }
 202                 else if (countfile != "") {
 203             CountTable ct;
 204             ct.readTable(countfile);
 205             nameMap = ct.getNameMap();
 206         }
 207
 208                 vector<unsigned long long> positions;
 209 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 210                 positions = m->divideFile(qualfile, processors);
 211                 for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(linePair(positions[i], positions[(i+1)]));      }
 212 #else
 213                 if (processors == 1) {
 214                         lines.push_back(linePair(0, 1000));
 215                 }else {
 216                         positions = m->setFilePosFasta(qualfile, numSeqs);
 217             if (positions.size() < processors) { processors = positions.size(); }
 218
 219                         //figure out how many sequences you have to process
 220                         int numSeqsPerProcessor = numSeqs / processors;
 221                         for (int i = 0; i < processors; i++) {
 222                                 int startIndex =  i * numSeqsPerProcessor;
 223                                 if(i == (processors - 1)){      numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 224                                 lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 225                         }
 226                 }
 227 #endif
 228
 229
 230                 if(processors == 1){ numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[0]);  }
 231                 else{  numSeqs = createProcessesCreateSummary(position, averageQ, scores, qualfile);  }
 232
 233                 if (m->control_pressed) {  return 0; }
 234
 235                 //print summary file
 236                 string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("summary");
 237                 printQual(summaryFile, position, averageQ, scores);
 238
 239                 if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
 240
 241                 //output results to screen
 242                 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
 243                 m->mothurOutEndLine();
 244                 m->mothurOut("Position\tNumSeqs\tAverageQ"); m->mothurOutEndLine();
 245                 for (int i = 0; i < position.size(); i+=100) {
 246                         float average = averageQ[i] / (float) position[i];
 247                         cout << i << '\t' << position[i] << '\t' << average;
 248                         m->mothurOutJustToLog(toString(i) + "\t" + toString(position[i]) + "\t" + toString(average)); m->mothurOutEndLine();
 249                 }
 250
 251                 m->mothurOutEndLine();
 252                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 253                 m->mothurOutEndLine();
 254                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 255                 m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
 256                 m->mothurOutEndLine();
 257
 258                 return 0;
 259         }
 260         catch(exception& e) {
 261                 m->errorOut(e, "SummaryQualCommand", "execute");
 262                 exit(1);
 263         }
 264 }
 265 /**************************************************************************************/
 266 int SummaryQualCommand::driverCreateSummary(vector<int>& position, vector<int>& averageQ, vector< vector<int> >& scores, string filename, linePair filePos) {
 267         try {
 268                 ifstream in;
 269                 m->openInputFile(filename, in);
 270
 271                 in.seekg(filePos.start);
 272
 273                 bool done = false;
 274                 int count = 0;
 275
 276                 while (!done) {
 277
 278                         if (m->control_pressed) { in.close(); return 1; }
 279
 280                         QualityScores current(in); m->gobble(in);
 281
 282                         if (current.getName() != "") {
 283
 284                                 int num = 1;
 285                                 if ((namefile != "") || (countfile != "")) {
 286                                         //make sure this sequence is in the namefile, else error
 287                                         map<string, int>::iterator it = nameMap.find(current.getName());
 288
 289                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 290                                         else { num = it->second; }
 291                                 }
 292
 293                                 vector<int> thisScores = current.getQualityScores();
 294
 295                                 //resize to num of positions setting number of seqs with that size to 1
 296                                 if (position.size() < thisScores.size()) { position.resize(thisScores.size(), 0); }
 297                                 if (averageQ.size() < thisScores.size()) { averageQ.resize(thisScores.size(), 0); }
 298                                 if (scores.size() < thisScores.size()) {
 299                                         scores.resize(thisScores.size());
 300                                         for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
 301                                 }
 302
 303                                 //increase counts of number of seqs with this position
 304                                 //average is really the total, we will average in execute
 305                                 for (int i = 0; i < thisScores.size(); i++) {
 306                                         position[i] += num;
 307                                         averageQ[i] += (thisScores[i] * num); //weighting for namesfile
 308                                         if (thisScores[i] > 40) { m->mothurOut("[ERROR]: " + current.getName() + " has a quality scores of " + toString(thisScores[i]) + ", expecting values to be less than 40."); m->mothurOutEndLine(); m->control_pressed = true; }
 309                                         else { scores[i][thisScores[i]] += num; }
 310                                 }
 311
 312                                 count += num;
 313                         }
 314
 315 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 316                         unsigned long long pos = in.tellg();
 317                         if ((pos == -1) || (pos >= filePos.end)) { break; }
 318 #else
 319                         if (in.eof()) { break; }
 320 #endif
 321                 }
 322
 323                 in.close();
 324
 325                 return count;
 326         }
 327         catch(exception& e) {
 328                 m->errorOut(e, "SummaryQualCommand", "driverCreateSummary");
 329                 exit(1);
 330         }
 331 }
 332 /**************************************************************************************************/
 333 int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vector<int>& averageQ, vector< vector<int> >& scores, string filename) {
 334         try {
 335                 int process = 1;
 336                 int numSeqs = 0;
 337                 processIDS.clear();
 338
 339 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 340
 341                 //loop through and create all the processes you want
 342                 while (process != processors) {
 343                         int pid = fork();
 344
 345                         if (pid > 0) {
 346                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 347                                 process++;
 348                         }else if (pid == 0){
 349                                 numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[process]);
 350
 351                                 //pass numSeqs to parent
 352                                 ofstream out;
 353                                 string tempFile = qualfile + toString(getpid()) + ".num.temp";
 354                                 m->openOutputFile(tempFile, out);
 355
 356                                 out << numSeqs << endl;
 357                                 out << position.size() << endl;
 358                                 for (int k = 0; k < position.size(); k++)                       {               out << position[k] << '\t'; }  out << endl;
 359                                 for (int k = 0; k < averageQ.size(); k++)                       {               out << averageQ[k] << '\t'; }  out << endl;
 360                                 for (int k = 0; k < scores.size(); k++) {
 361                                         for (int j = 0; j < 41; j++) {
 362                                                 out << scores[k][j] << '\t';
 363                                         }
 364                                         out << endl;
 365                                 }
 366                                 out << endl;
 367
 368                                 out.close();
 369
 370                                 exit(0);
 371                         }else {
 372                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 373                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 374                                 exit(0);
 375                         }
 376                 }
 377
 378                 //do your part
 379                 numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[0]);
 380
 381                 //force parent to wait until all the processes are done
 382                 for (int i=0;i<processIDS.size();i++) {
 383                         int temp = processIDS[i];
 384                         wait(&temp);
 385                 }
 386
 387                 //parent reads in and combine Filter info
 388                 for (int i = 0; i < processIDS.size(); i++) {
 389                         string tempFilename = qualfile + toString(processIDS[i]) + ".num.temp";
 390                         ifstream in;
 391                         m->openInputFile(tempFilename, in);
 392
 393                         int temp, tempNum;
 394                         in >> tempNum; m->gobble(in); numSeqs += tempNum;
 395                         in >> tempNum; m->gobble(in);
 396
 397                         if (position.size() < tempNum) { position.resize(tempNum, 0); }
 398                         if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }
 399                         if (scores.size() < tempNum) {
 400                                 scores.resize(tempNum);
 401                                 for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
 402                         }
 403
 404                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; position[k] += temp;                        }               m->gobble(in);
 405                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; averageQ[k] += temp;                }               m->gobble(in);
 406                         for (int k = 0; k < tempNum; k++)                       {
 407                                 for (int j = 0; j < 41; j++) {
 408                                         in >> temp; scores[k][j] += temp;
 409                                         m->gobble(in);
 410                                 }
 411                         }
 412
 413                         in.close();
 414                         m->mothurRemove(tempFilename);
 415                 }
 416
 417 #else
 418                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 419                 //Windows version shared memory, so be careful when passing variables through the seqSumQualData struct.
 420                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 421                 //Taking advantage of shared memory to pass results vectors.
 422                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 423
 424                 vector<seqSumQualData*> pDataArray;
 425                 DWORD   dwThreadIdArray[processors];
 426                 HANDLE  hThreadArray[processors];
 427
 428         bool hasNameMap = false;
 429         if ((namefile !="") || (countfile != "")) { hasNameMap = true; }
 430
 431                 //Create processor worker threads.
 432                 for( int i=0; i<processors; i++ ){
 433
 434                         // Allocate memory for thread data.
 435                         seqSumQualData* tempSum = new seqSumQualData(filename, m, lines[i].start, lines[i].end, hasNameMap, nameMap);
 436                         pDataArray.push_back(tempSum);
 437                         processIDS.push_back(i);
 438
 439                         hThreadArray[i] = CreateThread(NULL, 0, MySeqSumQualThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 440                 }
 441
 442                 //Wait until all threads have terminated.
 443                 WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
 444
 445                 //Close all thread handles and free memory allocations.
 446                 for(int i=0; i < pDataArray.size(); i++){
 447                         numSeqs += pDataArray[i]->count;
 448             int tempNum = pDataArray[i]->position.size();
 449             if (position.size() < tempNum) { position.resize(tempNum, 0); }
 450                         if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }
 451                         if (scores.size() < tempNum) {
 452                                 scores.resize(tempNum);
 453                                 for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
 454                         }
 455
 456             for (int k = 0; k < tempNum; k++)                   {                position[k]    +=  pDataArray[i]->position[k];         }
 457                         for (int k = 0; k < tempNum; k++)                       {                averageQ[k]    +=  pDataArray[i]->averageQ[k];         }
 458                         for (int k = 0; k < tempNum; k++)                       {       for (int j = 0; j < 41; j++) {  scores[k][j] += pDataArray[i]->scores[k][j];   }        }
 459
 460                         CloseHandle(hThreadArray[i]);
 461                         delete pDataArray[i];
 462                 }
 463 #endif
 464                 return numSeqs;
 465         }
 466         catch(exception& e) {
 467                 m->errorOut(e, "SummaryQualCommand", "createProcessesCreateSummary");
 468                 exit(1);
 469         }
 470 }
 471 /**************************************************************************************************/
 472 int SummaryQualCommand::printQual(string sumFile, vector<int>& position, vector<int>& averageQ, vector< vector<int> >& scores) {
 473         try {
 474                 ofstream out;
 475                 m->openOutputFile(sumFile, out);
 476                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 477                 outputNames.push_back(sumFile); outputTypes["summary"].push_back(sumFile);
 478
 479                 //print headings
 480                 out << "Position\tnumSeqs\tAverageQ\t";
 481                 for (int i = 0; i < 41; i++) { out << "q" << i << '\t'; }
 482                 out << endl;
 483
 484                 for (int i = 0; i < position.size(); i++) {
 485
 486                         if (m->control_pressed) { out.close(); return 0; }
 487
 488                         double average = averageQ[i] / (float) position[i];
 489                         out << i << '\t' << position[i] << '\t' << average << '\t';
 490
 491                         for (int j = 0; j < 41; j++) {
 492                                 out << scores[i][j] << '\t';
 493                         }
 494                         out << endl;
 495                 }
 496
 497                 out.close();
 498
 499                 return 0;
 500         }
 501         catch(exception& e) {
 502                 m->errorOut(e, "SummaryQualCommand", "printQual");
 503                 exit(1);
 504         }
 505 }
 506
 507 /**************************************************************************************/
 508
 509