trimflowscommand.cpp

   1 /*
   2  *  trimflowscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 12/22/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "trimflowscommand.h"
  11 #include "needlemanoverlap.hpp"
  12
  13 //**********************************************************************************************************************
  14
  15 vector<string> TrimFlowsCommand::getValidParameters(){
  16         try {
  17                 string Array[] =  {"flow", "totalflows", "minflows",
  18                         "fasta", "minlength", "maxlength", "maxhomop", "signal", "noise"
  19                         "oligos", "pdiffs", "bdiffs", "tdiffs",
  20                         "allfiles", "processors",
  21
  22
  23
  24 //                      "group",
  25                         "outputdir","inputdir"
  26
  27                 };
  28                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "TrimFlowsCommand", "getValidParameters");
  33                 exit(1);
  34         }
  35 }
  36
  37 //**********************************************************************************************************************
  38
  39 vector<string> TrimFlowsCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"flow"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "TrimFlowsCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50
  51 //**********************************************************************************************************************
  52
  53 vector<string> TrimFlowsCommand::getRequiredFiles(){
  54         try {
  55                 vector<string> myArray;
  56                 return myArray;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "TrimFlowsCommand", "getRequiredFiles");
  60                 exit(1);
  61         }
  62 }
  63
  64 //**********************************************************************************************************************
  65
  66 TrimFlowsCommand::TrimFlowsCommand(){
  67         try {
  68                 abort = true;
  69                 //initialize outputTypes
  70                 vector<string> tempOutNames;
  71                 outputTypes["flow"] = tempOutNames;
  72                 outputTypes["fasta"] = tempOutNames;
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
  76                 exit(1);
  77         }
  78 }
  79
  80 //***************************************************************************************************************
  81
  82 TrimFlowsCommand::~TrimFlowsCommand(){  /*      do nothing      */      }
  83
  84 //***************************************************************************************************************
  85
  86 void TrimFlowsCommand::help(){
  87         try {
  88                 m->mothurOut("The trim.flows command reads a flowgram file and creates .....\n");
  89                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
  90                 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n\n");
  91
  92         }
  93         catch(exception& e) {
  94                 m->errorOut(e, "TrimFlowsCommand", "help");
  95                 exit(1);
  96         }
  97 }
  98
  99 //**********************************************************************************************************************
 100
 101 TrimFlowsCommand::TrimFlowsCommand(string option)  {
 102         try {
 103
 104                 abort = false;
 105                 comboStarts = 0;
 106
 107                 //allow user to run help
 108                 if(option == "help") { help(); abort = true; }
 109
 110                 else {
 111                         //valid paramters for this command
 112                         string AlignArray[] =  {"flow", "totalflows", "minflows",
 113                                 "fasta", "minlength", "maxlength", "maxhomop", "signal", "noise",
 114                                 "oligos", "pdiffs", "bdiffs", "tdiffs",
 115                                 "allfiles", "processors",
 116
 117                                 //                      "group",
 118                                 "outputdir","inputdir"
 119
 120                         };
 121
 122                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
 123
 124                         OptionParser parser(option);
 125                         map<string,string> parameters = parser.getParameters();
 126
 127                         ValidParameters validParameter;
 128                         map<string,string>::iterator it;
 129
 130                         //check to make sure all parameters are valid for command
 131                         for (it = parameters.begin(); it != parameters.end(); it++) {
 132                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 133                         }
 134
 135                         //initialize outputTypes
 136                         vector<string> tempOutNames;
 137                         outputTypes["flow"] = tempOutNames;
 138                         outputTypes["fasta"] = tempOutNames;
 139
 140                         //if the user changes the input directory command factory will send this info to us in the output parameter
 141                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 142                         if (inputDir == "not found"){   inputDir = "";          }
 143                         else {
 144                                 string path;
 145                                 it = parameters.find("flow");
 146                                 //user has given a template file
 147                                 if(it != parameters.end()){
 148                                         path = m->hasPath(it->second);
 149                                         //if the user has not given a path then, add inputdir. else leave path alone.
 150                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 151                                 }
 152
 153                                 it = parameters.find("oligos");
 154                                 //user has given a template file
 155                                 if(it != parameters.end()){
 156                                         path = m->hasPath(it->second);
 157                                         //if the user has not given a path then, add inputdir. else leave path alone.
 158                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 159                                 }
 160
 161
 162 //                              it = parameters.find("group");
 163 //                              //user has given a template file
 164 //                              if(it != parameters.end()){
 165 //                                      path = m->hasPath(it->second);
 166 //                                      //if the user has not given a path then, add inputdir. else leave path alone.
 167 //                                      if (path == "") {       parameters["group"] = inputDir + it->second;            }
 168 //                              }
 169                         }
 170
 171
 172                         //check for required parameters
 173                         flowFileName = validParameter.validFile(parameters, "flow", true);
 174                         if (flowFileName == "not found") { m->mothurOut("flow is a required parameter for the trim.flows command."); m->mothurOutEndLine(); abort = true; }
 175                         else if (flowFileName == "not open") { abort = true; }
 176
 177                         //if the user changes the output directory command factory will send this info to us in the output parameter
 178                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 179                                 outputDir = "";
 180                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 181                         }
 182
 183
 184                         //check for optional parameter and set defaults
 185                         // ...at some point should added some additional type checking...
 186
 187                         string temp;
 188                         temp = validParameter.validFile(parameters, "minflows", false);         if (temp == "not found") { temp = "360"; }
 189                         convert(temp, minFlows);
 190
 191                         temp = validParameter.validFile(parameters, "totalflows", false);       if (temp == "not found") { temp = "720"; }
 192                         convert(temp, totalFlows);
 193
 194
 195                         temp = validParameter.validFile(parameters, "oligos", true);
 196                         if (temp == "not found")        {       oligoFileName = "";             }
 197                         else if(temp == "not open")     {       abort = true;                   }
 198                         else                                            {       oligoFileName = temp;   }
 199
 200                         temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
 201                         else if(m->isTrue(temp))        {       fasta = 1;      }
 202
 203                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
 204                         convert(temp, maxHomoP);
 205
 206                         temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
 207                         convert(temp, signal);
 208
 209                         temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
 210                         convert(temp, noise);
 211
 212                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found"){       temp = "0";             }
 213                         convert(temp, minLength);
 214
 215                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found"){       temp = "0";             }
 216                         convert(temp, maxLength);
 217
 218                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
 219                         convert(temp, bdiffs);
 220
 221                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
 222                         convert(temp, pdiffs);
 223
 224                         temp = validParameter.validFile(parameters, "tdiffs", false);
 225                         if (temp == "not found"){ int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 226                         convert(temp, tdiffs);
 227                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 228
 229                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "T";          }
 230                         allFiles = m->isTrue(temp);
 231
 232                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found") { temp = "1"; }
 233                         convert(temp, processors);
 234
 235                         if(oligoFileName == ""){        allFiles = 0;           }
 236
 237                         numFPrimers = 0;
 238                         numRPrimers = 0;
 239                 }
 240
 241         }
 242         catch(exception& e) {
 243                 m->errorOut(e, "TrimFlowsCommand", "TrimSeqsCommand");
 244                 exit(1);
 245         }
 246 }
 247
 248 //***************************************************************************************************************
 249
 250 int TrimFlowsCommand::execute(){
 251         try{
 252
 253                 if (abort == true) { return 0; }
 254
 255                 string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
 256                 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
 257
 258                 string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap.flow";
 259                 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 260
 261                 string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.fasta";
 262                 if(fasta){
 263                         outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
 264                 }
 265
 266                 vector<unsigned long int> flowFilePos = getFlowFileBreaks();
 267                 for (int i = 0; i < (flowFilePos.size()-1); i++) {
 268                         lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
 269                 }
 270
 271                 vector<vector<string> > barcodePrimerComboFileNames;
 272                 if(oligoFileName != ""){
 273                         getOligos(barcodePrimerComboFileNames);
 274                 }
 275
 276 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 277                 if(processors == 1){
 278                         driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 279                 }else{
 280                         createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
 281                 }
 282 #else
 283                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 284 #endif
 285
 286                 if (m->control_pressed) {  return 0; }
 287
 288                 if(allFiles){
 289
 290                         ofstream output;
 291                         string flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
 292                         m->openOutputFile(flowFilesFileName, output);
 293
 294                         for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 295                                 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 296
 297                                         FILE * pFile;
 298                                         unsigned long int size;
 299
 300                                         //get num bytes in file
 301                                         pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
 302                                         if (pFile==NULL) perror ("Error opening file");
 303                                         else{
 304                                                 fseek (pFile, 0, SEEK_END);
 305                                                 size=ftell (pFile);
 306                                                 fclose (pFile);
 307                                         }
 308
 309                                         if(size < 10){
 310 //                                              m->mothurOut("deleting: " + barcodePrimerComboFileNames[i][j] + '\n');
 311                                                 remove(barcodePrimerComboFileNames[i][j].c_str());
 312                                         }
 313                                         else{
 314 //                                              m->mothurOut("saving: " + barcodePrimerComboFileNames[i][j] + '\n');
 315                                                 output << barcodePrimerComboFileNames[i][j] << endl;
 316                                         }
 317                                 }
 318                         }
 319                         output.close();
 320                 }
 321
 322                 m->mothurOutEndLine();
 323                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 324                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 325                 m->mothurOutEndLine();
 326
 327                 return 0;
 328         }
 329         catch(exception& e) {
 330                 m->errorOut(e, "TrimSeqsCommand", "execute");
 331                 exit(1);
 332         }
 333 }
 334
 335 //***************************************************************************************************************
 336
 337 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames, linePair* line){
 338
 339         try {
 340
 341                 ofstream trimFlowFile;
 342                 m->openOutputFile(trimFlowFileName, trimFlowFile);
 343                 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 344
 345                 ofstream scrapFlowFile;
 346                 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
 347                 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
 348
 349                 if(line->start == 4){
 350                         scrapFlowFile << totalFlows << endl;
 351                         trimFlowFile << totalFlows << endl;
 352                         for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 353                                 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 354                                         //                              barcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
 355                                         ofstream temp;
 356                                         m->openOutputFile(barcodePrimerComboFileNames[i][j], temp);
 357                                         temp << totalFlows << endl;
 358                                         temp.close();
 359                                 }
 360                         }
 361                 }
 362
 363                 FlowData flowData(numFlows, signal, noise, maxHomoP);
 364
 365                 ofstream fastaFile;
 366                 if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }
 367
 368                 ifstream flowFile;
 369                 m->openInputFile(flowFileName, flowFile);
 370
 371                 flowFile.seekg(line->start);
 372
 373                 int count = 0;
 374                 bool moreSeqs = 1;
 375
 376                 while(moreSeqs) {
 377
 378                         int success = 1;
 379                         int currentSeqDiffs = 0;
 380                         string trashCode = "";
 381
 382                         flowData.getNext(flowFile);
 383                         flowData.capFlows(totalFlows);
 384
 385                         Sequence currSeq = flowData.getSequence();
 386                         if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
 387                                 success = 0;
 388                                 trashCode += 'l';
 389                         }
 390
 391                         if(minLength > 0 || maxLength > 0){     //screen to see if sequence is above and below a specific number of bases
 392                                 int seqLength = currSeq.getNumBases();
 393                                 if(seqLength < minLength || seqLength > maxLength){
 394                                         success = 0;
 395                                         trashCode += 'l';
 396                                 }
 397                         }
 398
 399                         int primerIndex, barcodeIndex;
 400
 401                         if(barcodes.size() != 0){
 402                                 success = stripBarcode(currSeq, barcodeIndex);
 403                                 if(success > bdiffs)            {       trashCode += 'b';       }
 404                                 else{ currentSeqDiffs += success;  }
 405                         }
 406
 407                         if(numFPrimers != 0){
 408                                 success = stripForward(currSeq, primerIndex);
 409                                 if(success > pdiffs)            {       trashCode += 'f';       }
 410                                 else{ currentSeqDiffs += success;  }
 411                         }
 412
 413                         if (currentSeqDiffs > tdiffs)   {       trashCode += 't';   }
 414
 415                         if(numRPrimers != 0){
 416                                 success = stripReverse(currSeq);
 417                                 if(!success)                            {       trashCode += 'r';       }
 418                         }
 419
 420
 421                         if(trashCode.length() == 0){
 422                                 flowData.printFlows(trimFlowFile);
 423
 424                                 if(fasta){
 425                                         currSeq.printSequence(fastaFile);
 426                                 }
 427
 428                                 if(barcodes.size() != 0 || primers.size() != 0){
 429 //                                      string fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + barcodePrimerCombos[barcodeIndex][primerIndex] + ".flow";
 430                                         ofstream output;
 431                                         m->openOutputFileAppend(barcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 432                                         output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 433
 434                                         flowData.printFlows(output);
 435                                         output.close();
 436                                 }
 437
 438                         }
 439                         else{
 440                                 flowData.printFlows(scrapFlowFile, trashCode);
 441                         }
 442
 443                         count++;
 444
 445                         //report progress
 446                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 447
 448 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 449                         unsigned long int pos = flowFile.tellg();
 450
 451                         if ((pos == -1) || (pos >= line->end)) { break; }
 452 #else
 453                         if (flowFile.eof()) { break; }
 454 #endif
 455
 456                 }
 457                 //report progress
 458                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 459
 460                 trimFlowFile.close();
 461                 scrapFlowFile.close();
 462                 flowFile.close();
 463                 if(fasta){      fastaFile.close();      }
 464
 465                 return count;
 466         }
 467         catch(exception& e) {
 468                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 469                 exit(1);
 470         }
 471 }
 472
 473 //***************************************************************************************************************
 474
 475 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 476         try {
 477                 ifstream oligosFile;
 478                 m->openInputFile(oligoFileName, oligosFile);
 479
 480                 string type, oligo, group;
 481
 482                 int indexPrimer = 0;
 483                 int indexBarcode = 0;
 484
 485                 while(!oligosFile.eof()){
 486
 487                         oligosFile >> type; m->gobble(oligosFile);      //get the first column value of the row - is it a comment or a feature we are interested in?
 488
 489                         if(type[0] == '#'){     //igore the line because there's a comment
 490                                 while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       } // get rest of line if there's any crap there
 491                         }
 492                         else{                           //there's a feature we're interested in
 493
 494                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 495
 496                                 oligosFile >> oligo;    //get the DNA sequence for the feature
 497
 498                                 for(int i=0;i<oligo.length();i++){      //make type case insensitive and change any U's to T's
 499                                         oligo[i] = toupper(oligo[i]);
 500                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 501                                 }
 502
 503                                 if(type == "FORWARD"){  //if the feature is a forward primer...
 504                                         group = "";
 505
 506                                         while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
 507                                                 char c = oligosFile.get();
 508                                                 if (c == 10 || c == 13){        break;  }
 509                                                 else if (c == 32 || c == 9){;} //space or tab
 510                                                 else {  group += c;  }
 511                                         }
 512
 513                                         //have we seen this primer already?
 514                                         map<string, int>::iterator itPrimer = primers.find(oligo);
 515                                         if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 516
 517                                         primers[oligo]=indexPrimer; indexPrimer++;
 518                                         primerNameVector.push_back(group);
 519
 520                                 }
 521                                 else if(type == "REVERSE"){
 522                                         Sequence oligoRC("reverse", oligo);
 523                                         oligoRC.reverseComplement();
 524                                         revPrimer.push_back(oligoRC.getUnaligned());
 525                                 }
 526                                 else if(type == "BARCODE"){
 527                                         oligosFile >> group;
 528
 529                                         //check for repeat barcodes
 530                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 531                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 532
 533                                         barcodes[oligo]=indexBarcode; indexBarcode++;
 534                                         barcodeNameVector.push_back(group);
 535                                 }
 536                                 else{
 537                                         m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
 538                                 }
 539                         }
 540
 541                         m->gobble(oligosFile);
 542                 }
 543                 oligosFile.close();
 544
 545                 //add in potential combos
 546                 outFlowFileNames.resize(barcodeNameVector.size());
 547                 for(int i=0;i<outFlowFileNames.size();i++){
 548                         outFlowFileNames[i].assign(primerNameVector.size(), "");
 549                 }
 550
 551                 if(allFiles){
 552                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 553                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 554
 555                                         string primerName = primerNameVector[itPrimer->second];
 556                                         string barcodeName = barcodeNameVector[itBar->second];
 557
 558                                         string comboGroupName = "";
 559                                         string fileName = "";
 560
 561                                         if(primerName == ""){
 562                                                 comboGroupName = barcodeNameVector[itBar->second];
 563                                                 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
 564                                         }
 565                                         else{
 566                                                 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
 567                                                 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
 568                                         }
 569
 570                                         outputNames.push_back(fileName);
 571                                         outputTypes["flow"].push_back(fileName);
 572                                         outFlowFileNames[itBar->second][itPrimer->second] = fileName;
 573
 574                                         ofstream temp;
 575                                         m->openOutputFile(fileName, temp);
 576                                         temp.close();
 577                                 }
 578                         }
 579                 }
 580
 581                 numFPrimers = primers.size();
 582                 numRPrimers = revPrimer.size();
 583
 584         }
 585         catch(exception& e) {
 586                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 587                 exit(1);
 588         }
 589 }
 590
 591 //***************************************************************************************************************
 592
 593 int TrimFlowsCommand::stripBarcode(Sequence& seq, int& group){
 594         try {
 595
 596                 string rawSequence = seq.getUnaligned();
 597                 int success = bdiffs + 1;       //guilty until proven innocent
 598
 599                 //can you find the barcode
 600                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 601                         string oligo = it->first;
 602                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 603                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 604                                 break;
 605                         }
 606
 607                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 608                                 group = it->second;
 609                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 610
 611                                 success = 0;
 612                                 break;
 613                         }
 614                 }
 615
 616                 //if you found the barcode or if you don't want to allow for diffs
 617                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 618
 619                 else { //try aligning and see if you can find it
 620
 621                         int maxLength = 0;
 622
 623                         Alignment* alignment;
 624                         if (barcodes.size() > 0) {
 625                                 map<string,int>::iterator it=barcodes.begin();
 626
 627                                 for(it;it!=barcodes.end();it++){
 628                                         if(it->first.length() > maxLength){
 629                                                 maxLength = it->first.length();
 630                                         }
 631                                 }
 632                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
 633
 634                         }else{ alignment = NULL; }
 635
 636                         //can you find the barcode
 637                         int minDiff = 1e6;
 638                         int minCount = 1;
 639                         int minGroup = -1;
 640                         int minPos = 0;
 641
 642                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 643                                 string oligo = it->first;
 644                                 //                              int length = oligo.length();
 645
 646                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 647                                         success = bdiffs + 10;
 648                                         break;
 649                                 }
 650
 651                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 652                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 653                                 oligo = alignment->getSeqAAln();
 654                                 string temp = alignment->getSeqBAln();
 655
 656                                 int alnLength = oligo.length();
 657
 658                                 for(int i=oligo.length()-1;i>=0;i--){
 659                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 660                                 }
 661                                 oligo = oligo.substr(0,alnLength);
 662                                 temp = temp.substr(0,alnLength);
 663
 664                                 int numDiff = countDiffs(oligo, temp);
 665
 666                                 if(numDiff < minDiff){
 667                                         minDiff = numDiff;
 668                                         minCount = 1;
 669                                         minGroup = it->second;
 670                                         minPos = 0;
 671                                         for(int i=0;i<alnLength;i++){
 672                                                 if(temp[i] != '-'){
 673                                                         minPos++;
 674                                                 }
 675                                         }
 676                                 }
 677                                 else if(numDiff == minDiff){
 678                                         minCount++;
 679                                 }
 680
 681                         }
 682
 683                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
 684                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
 685                         else{                                                                                                   //use the best match
 686                                 group = minGroup;
 687                                 seq.setUnaligned(rawSequence.substr(minPos));
 688                                 success = minDiff;
 689                         }
 690
 691                         if (alignment != NULL) {  delete alignment;  }
 692
 693                 }
 694
 695                 return success;
 696
 697         }
 698         catch(exception& e) {
 699                 m->errorOut(e, "TrimFlowsCommand", "stripBarcode");
 700                 exit(1);
 701         }
 702
 703 }
 704
 705 //***************************************************************************************************************
 706
 707 int TrimFlowsCommand::stripForward(Sequence& seq, int& group){
 708         try {
 709
 710                 string rawSequence = seq.getUnaligned();
 711                 int success = pdiffs + 1;       //guilty until proven innocent
 712
 713                 //can you find the primer
 714                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 715                         string oligo = it->first;
 716                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
 717                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 718                                 break;
 719                         }
 720
 721                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 722                                 group = it->second;
 723                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 724                                 success = 0;
 725                                 break;
 726                         }
 727                 }
 728
 729                 //if you found the barcode or if you don't want to allow for diffs
 730                 if ((pdiffs == 0) || (success == 0)) { return success;  }
 731
 732                 else { //try aligning and see if you can find it
 733
 734                         int maxLength = 0;
 735
 736                         Alignment* alignment;
 737                         if (primers.size() > 0) {
 738                                 map<string,int>::iterator it=primers.begin();
 739
 740                                 for(it;it!=primers.end();it++){
 741                                         if(it->first.length() > maxLength){
 742                                                 maxLength = it->first.length();
 743                                         }
 744                                 }
 745                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
 746
 747                         }else{ alignment = NULL; }
 748
 749                         //can you find the barcode
 750                         int minDiff = 1e6;
 751                         int minCount = 1;
 752                         int minGroup = -1;
 753                         int minPos = 0;
 754
 755                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 756                                 string oligo = it->first;
 757                                 //                              int length = oligo.length();
 758
 759                                 if(rawSequence.length() < maxLength){
 760                                         success = pdiffs + 100;
 761                                         break;
 762                                 }
 763
 764                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 765                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 766                                 oligo = alignment->getSeqAAln();
 767                                 string temp = alignment->getSeqBAln();
 768
 769                                 int alnLength = oligo.length();
 770
 771                                 for(int i=oligo.length()-1;i>=0;i--){
 772                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 773                                 }
 774                                 oligo = oligo.substr(0,alnLength);
 775                                 temp = temp.substr(0,alnLength);
 776
 777                                 int numDiff = countDiffs(oligo, temp);
 778
 779                                 if(numDiff < minDiff){
 780                                         minDiff = numDiff;
 781                                         minCount = 1;
 782                                         minGroup = it->second;
 783                                         minPos = 0;
 784                                         for(int i=0;i<alnLength;i++){
 785                                                 if(temp[i] != '-'){
 786                                                         minPos++;
 787                                                 }
 788                                         }
 789                                 }
 790                                 else if(numDiff == minDiff){
 791                                         minCount++;
 792                                 }
 793
 794                         }
 795
 796                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
 797                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
 798                         else{                                                                                                   //use the best match
 799                                 group = minGroup;
 800                                 seq.setUnaligned(rawSequence.substr(minPos));
 801                                 success = minDiff;
 802                         }
 803
 804                         if (alignment != NULL) {  delete alignment;  }
 805
 806                 }
 807
 808                 return success;
 809
 810         }
 811         catch(exception& e) {
 812                 m->errorOut(e, "TrimFlowsCommand", "stripForward");
 813                 exit(1);
 814         }
 815 }
 816
 817 //***************************************************************************************************************
 818
 819 bool TrimFlowsCommand::stripReverse(Sequence& seq){
 820         try {
 821
 822                 string rawSequence = seq.getUnaligned();
 823                 bool success = 0;       //guilty until proven innocent
 824
 825                 for(int i=0;i<numRPrimers;i++){
 826                         string oligo = revPrimer[i];
 827
 828                         if(rawSequence.length() < oligo.length()){
 829                                 success = 0;
 830                                 break;
 831                         }
 832
 833                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 834                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 835                                 success = 1;
 836                                 break;
 837                         }
 838                 }
 839
 840                 return success;
 841
 842         }
 843         catch(exception& e) {
 844                 m->errorOut(e, "TrimFlowsCommand", "stripReverse");
 845                 exit(1);
 846         }
 847 }
 848
 849
 850 //***************************************************************************************************************
 851
 852 bool TrimFlowsCommand::compareDNASeq(string oligo, string seq){
 853         try {
 854                 bool success = 1;
 855                 int length = oligo.length();
 856
 857                 for(int i=0;i<length;i++){
 858
 859                         if(oligo[i] != seq[i]){
 860                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 861                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 862                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 863                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 864                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 865                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 866                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 867                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 868                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 869                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 870                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 871                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 872
 873                                 if(success == 0)        {       break;   }
 874                         }
 875                         else{
 876                                 success = 1;
 877                         }
 878                 }
 879
 880                 return success;
 881         }
 882         catch(exception& e) {
 883                 m->errorOut(e, "TrimFlowsCommand", "compareDNASeq");
 884                 exit(1);
 885         }
 886
 887 }
 888
 889 //***************************************************************************************************************
 890
 891 int TrimFlowsCommand::countDiffs(string oligo, string seq){
 892         try {
 893
 894                 int length = oligo.length();
 895                 int countDiffs = 0;
 896
 897                 for(int i=0;i<length;i++){
 898
 899                         if(oligo[i] != seq[i]){
 900                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
 901                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
 902                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
 903                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
 904                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
 905                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
 906                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
 907                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
 908                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 909                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 910                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
 911                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
 912                         }
 913
 914                 }
 915
 916                 return countDiffs;
 917         }
 918         catch(exception& e) {
 919                 m->errorOut(e, "TrimFlowsCommand", "countDiffs");
 920                 exit(1);
 921         }
 922
 923 }
 924
 925 /**************************************************************************************************/
 926
 927 vector<unsigned long int> TrimFlowsCommand::getFlowFileBreaks() {
 928
 929         try{
 930
 931                 vector<unsigned long int> filePos;
 932                 filePos.push_back(0);
 933
 934                 FILE * pFile;
 935                 unsigned long int size;
 936
 937                 //get num bytes in file
 938                 pFile = fopen (flowFileName.c_str(),"rb");
 939                 if (pFile==NULL) perror ("Error opening file");
 940                 else{
 941                         fseek (pFile, 0, SEEK_END);
 942                         size=ftell (pFile);
 943                         fclose (pFile);
 944                 }
 945
 946                 //estimate file breaks
 947                 unsigned long int chunkSize = 0;
 948                 chunkSize = size / processors;
 949
 950                 //file too small to divide by processors
 951                 if (chunkSize == 0)  {  processors = 1; filePos.push_back(size); return filePos;        }
 952
 953                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 954                 for (int i = 0; i < processors; i++) {
 955                         unsigned long int spot = (i+1) * chunkSize;
 956
 957                         ifstream in;
 958                         m->openInputFile(flowFileName, in);
 959                         in.seekg(spot);
 960
 961                         string dummy = m->getline(in);
 962
 963                         //there was not another sequence before the end of the file
 964                         unsigned long int sanityPos = in.tellg();
 965
 966 //                      if (sanityPos == -1) {  break;  }
 967 //                      else {  filePos.push_back(newSpot);  }
 968                         if (sanityPos == -1) {  break;  }
 969                         else {  filePos.push_back(sanityPos);  }
 970
 971                         in.close();
 972                 }
 973
 974                 //save end pos
 975                 filePos.push_back(size);
 976
 977                 //sanity check filePos
 978                 for (int i = 0; i < (filePos.size()-1); i++) {
 979                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 980                 }
 981
 982                 ifstream in;
 983                 m->openInputFile(flowFileName, in);
 984                 in >> numFlows;
 985                 m->gobble(in);
 986                 unsigned long int spot = in.tellg();
 987                 filePos[0] = spot;
 988                 in.close();
 989
 990                 processors = (filePos.size() - 1);
 991
 992                 return filePos;
 993         }
 994         catch(exception& e) {
 995                 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
 996                 exit(1);
 997         }
 998 }
 999
1000 /**************************************************************************************************/
1001
1002 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
1003
1004         try {
1005 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1006                 int process = 1;
1007                 int exitCommand = 1;
1008                 processIDS.clear();
1009
1010                 //loop through and create all the processes you want
1011                 while (process != processors) {
1012                         int pid = fork();
1013
1014                         if (pid > 0) {
1015                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1016                                 process++;
1017                         }else if (pid == 0){
1018
1019                                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
1020                                 for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
1021                                         for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
1022                                                 tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
1023                                                 ofstream temp;
1024                                                 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
1025                                                 temp.close();
1026
1027                                         }
1028                                 }
1029
1030                                 driverCreateTrim(flowFileName,
1031                                                                  (trimFlowFileName + toString(getpid()) + ".temp"),
1032                                                                  (scrapFlowFileName + toString(getpid()) + ".temp"),
1033                                                                  (fastaFileName + toString(getpid()) + ".temp"),
1034                                                                  tempBarcodePrimerComboFileNames, lines[process]);
1035
1036                                 exit(0);
1037                         }else {
1038                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1039                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1040                                 exit(0);
1041                         }
1042                 }
1043
1044                 //parent do my part
1045                 ofstream temp;
1046                 m->openOutputFile(trimFlowFileName, temp);
1047                 temp.close();
1048
1049                 m->openOutputFile(scrapFlowFileName, temp);
1050                 temp.close();
1051
1052                 if(fasta){
1053                         m->openOutputFile(fastaFileName, temp);
1054                         temp.close();
1055                 }
1056
1057                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
1058
1059                 //force parent to wait until all the processes are done
1060                 for (int i=0;i<processIDS.size();i++) {
1061                         int temp = processIDS[i];
1062                         wait(&temp);
1063                 }
1064
1065                 //append files
1066                 m->mothurOutEndLine();
1067                 for(int i=0;i<processIDS.size();i++){
1068
1069                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
1070
1071                         m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
1072                         remove((trimFlowFileName + toString(processIDS[i]) + ".temp").c_str());
1073 //                      m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
1074
1075                         m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
1076                         remove((scrapFlowFileName + toString(processIDS[i]) + ".temp").c_str());
1077 //                      m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
1078
1079                         if(fasta){
1080                                 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
1081                                 remove((fastaFileName + toString(processIDS[i]) + ".temp").c_str());
1082 //                              m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
1083                         }
1084                         if(allFiles){
1085                                 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
1086                                         for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
1087                                                 m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
1088                                                 remove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
1089                                         }
1090                                 }
1091                         }
1092                 }
1093
1094                 return exitCommand;
1095 #endif
1096         }
1097         catch(exception& e) {
1098                 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
1099                 exit(1);
1100         }
1101 }
1102
1103 //***************************************************************************************************************