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 vector<string> TrimFlowsCommand::setParameters(){
  15         try {
  16                 CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pflow);
  17                 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
  18                 CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
  19                 CommandParameter pmaxflows("maxflows", "Number", "", "720", "", "", "",false,false); parameters.push_back(pmaxflows);
  20                 CommandParameter pminflows("minflows", "Number", "", "360", "", "", "",false,false); parameters.push_back(pminflows);
  21                 CommandParameter pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
  22                 CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
  23                 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
  24                 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
  25                 CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
  26                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  27                 CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
  28                 CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
  29                 CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
  30                 CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
  31                 CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfasta);
  32                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  33                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  34
  35                 vector<string> myArray;
  36                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  37                 return myArray;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "TrimFlowsCommand", "setParameters");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 string TrimFlowsCommand::getHelpString(){
  46         try {
  47                 string helpString = "";
  48                 helpString += "The trim.flows command reads a flowgram file and creates .....\n";
  49                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  50                 helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n";
  51                 return helpString;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "TrimFlowsCommand", "getHelpString");
  55                 exit(1);
  56         }
  57 }
  58
  59 //**********************************************************************************************************************
  60
  61 TrimFlowsCommand::TrimFlowsCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65                 vector<string> tempOutNames;
  66                 outputTypes["flow"] = tempOutNames;
  67                 outputTypes["fasta"] = tempOutNames;
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75
  76 TrimFlowsCommand::TrimFlowsCommand(string option)  {
  77         try {
  78
  79                 abort = false; calledHelp = false;
  80                 comboStarts = 0;
  81
  82                 //allow user to run help
  83                 if(option == "help") { help(); abort = true; calledHelp = true; }
  84                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  85
  86                 else {
  87
  88                         vector<string> myArray = setParameters();
  89
  90                         OptionParser parser(option);
  91                         map<string,string> parameters = parser.getParameters();
  92
  93                         ValidParameters validParameter;
  94                         map<string,string>::iterator it;
  95
  96                         //check to make sure all parameters are valid for command
  97                         for (it = parameters.begin(); it != parameters.end(); it++) {
  98                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  99                         }
 100
 101                         //initialize outputTypes
 102                         vector<string> tempOutNames;
 103                         outputTypes["flow"] = tempOutNames;
 104                         outputTypes["fasta"] = tempOutNames;
 105
 106                         //if the user changes the input directory command factory will send this info to us in the output parameter
 107                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 108                         if (inputDir == "not found"){   inputDir = "";          }
 109                         else {
 110                                 string path;
 111                                 it = parameters.find("flow");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 117                                 }
 118
 119                                 it = parameters.find("oligos");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 125                                 }
 126
 127                         }
 128
 129
 130                         //check for required parameters
 131                         flowFileName = validParameter.validFile(parameters, "flow", true);
 132                         if (flowFileName == "not found") {
 133                                 flowFileName = m->getFlowFile();
 134                                 if (flowFileName != "") {  m->mothurOut("Using " + flowFileName + " as input file for the flow parameter."); m->mothurOutEndLine(); }
 135                                 else {
 136                                         m->mothurOut("No valid current flow file. You must provide a flow file."); m->mothurOutEndLine();
 137                                         abort = true;
 138                                 }
 139                         }else if (flowFileName == "not open") { flowFileName = ""; abort = true; }
 140
 141                         //if the user changes the output directory command factory will send this info to us in the output parameter
 142                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 143                                 outputDir = "";
 144                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 145                         }
 146
 147
 148                         //check for optional parameter and set defaults
 149                         // ...at some point should added some additional type checking...
 150
 151                         string temp;
 152                         temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
 153                         convert(temp, minFlows);
 154
 155                         temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
 156                         convert(temp, maxFlows);
 157
 158
 159                         temp = validParameter.validFile(parameters, "oligos", true);
 160                         if (temp == "not found")        {       oligoFileName = "";             }
 161                         else if(temp == "not open")     {       abort = true;                   }
 162                         else                                            {       oligoFileName = temp;   }
 163
 164                         temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
 165                         else if(m->isTrue(temp))        {       fasta = 1;      }
 166
 167                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
 168                         convert(temp, maxHomoP);
 169
 170                         temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
 171                         convert(temp, signal);
 172
 173                         temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
 174                         convert(temp, noise);
 175
 176                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found"){       temp = "0";             }
 177                         convert(temp, minLength);
 178
 179                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found"){       temp = "0";             }
 180                         convert(temp, maxLength);
 181
 182                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
 183                         convert(temp, bdiffs);
 184
 185                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
 186                         convert(temp, pdiffs);
 187
 188                         temp = validParameter.validFile(parameters, "tdiffs", false);
 189                         if (temp == "not found"){ int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 190                         convert(temp, tdiffs);
 191                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 192
 193                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found"){ temp = "T";           }
 194                         allFiles = m->isTrue(temp);
 195
 196                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 197                         m->setProcessors(temp);
 198                         convert(temp, processors);
 199
 200                         flowOrder = validParameter.validFile(parameters, "order", false);
 201                         if (flowOrder == "not found"){ flowOrder = "TACG";              }
 202                         else if(flowOrder.length() != 4){
 203                                 m->mothurOut("The value of the order option must be four bases long\n");
 204                         }
 205
 206                         if(oligoFileName == ""){        allFiles = 0;           }
 207
 208                         numFPrimers = 0;
 209                         numRPrimers = 0;
 210                 }
 211
 212         }
 213         catch(exception& e) {
 214                 m->errorOut(e, "TrimFlowsCommand", "TrimSeqsCommand");
 215                 exit(1);
 216         }
 217 }
 218
 219 //***************************************************************************************************************
 220
 221 int TrimFlowsCommand::execute(){
 222         try{
 223
 224                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 225
 226                 string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
 227                 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
 228
 229                 string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap.flow";
 230                 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 231
 232                 string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.fasta";
 233                 if(fasta){
 234                         outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
 235                 }
 236
 237                 vector<unsigned long int> flowFilePos = getFlowFileBreaks();
 238                 for (int i = 0; i < (flowFilePos.size()-1); i++) {
 239                         lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
 240                 }
 241
 242                 vector<vector<string> > barcodePrimerComboFileNames;
 243                 if(oligoFileName != ""){
 244                         getOligos(barcodePrimerComboFileNames);
 245                 }
 246
 247 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 248                 if(processors == 1){
 249                         driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 250                 }else{
 251                         createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
 252                 }
 253 #else
 254                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 255 #endif
 256
 257                 if (m->control_pressed) {  return 0; }
 258
 259                 string flowFilesFileName;
 260                 ofstream output;
 261
 262                 if(allFiles){
 263
 264                         flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
 265                         m->openOutputFile(flowFilesFileName, output);
 266
 267                         for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 268                                 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 269
 270                                         FILE * pFile;
 271                                         unsigned long int size;
 272
 273                                         //get num bytes in file
 274                                         pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
 275                                         if (pFile==NULL) perror ("Error opening file");
 276                                         else{
 277                                                 fseek (pFile, 0, SEEK_END);
 278                                                 size=ftell(pFile);
 279                                                 fclose (pFile);
 280                                         }
 281
 282                                         if(size < 10){
 283                                                 remove(barcodePrimerComboFileNames[i][j].c_str());
 284                                         }
 285                                         else{
 286                                                 output << barcodePrimerComboFileNames[i][j] << endl;
 287                                                 outputNames.push_back(barcodePrimerComboFileNames[i][j]);
 288                                                 outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
 289                                         }
 290                                 }
 291                         }
 292                         output.close();
 293                 }
 294                 else{
 295                         flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
 296                         m->openOutputFile(flowFilesFileName, output);
 297
 298                         output << trimFlowFileName << endl;
 299
 300                         output.close();
 301                 }
 302                 outputTypes["flow.files"].push_back(flowFilesFileName);
 303                 outputNames.push_back(flowFilesFileName);
 304
 305 //              set fasta file as new current fastafile
 306 //              string current = "";
 307 //              itTypes = outputTypes.find("fasta");
 308 //              if (itTypes != outputTypes.end()) {
 309 //                      if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 310 //              }
 311
 312                 m->mothurOutEndLine();
 313                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 314                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 315                 m->mothurOutEndLine();
 316
 317                 return 0;
 318         }
 319         catch(exception& e) {
 320                 m->errorOut(e, "TrimSeqsCommand", "execute");
 321                 exit(1);
 322         }
 323 }
 324
 325 //***************************************************************************************************************
 326
 327 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames, linePair* line){
 328
 329         try {
 330
 331                 ofstream trimFlowFile;
 332                 m->openOutputFile(trimFlowFileName, trimFlowFile);
 333                 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 334
 335                 ofstream scrapFlowFile;
 336                 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
 337                 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
 338
 339                 if(line->start == 4){
 340                         scrapFlowFile << maxFlows << endl;
 341                         trimFlowFile << maxFlows << endl;
 342                         if(allFiles){
 343                                 for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 344                                         for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 345                                                 //                              barcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
 346                                                 ofstream temp;
 347                                                 m->openOutputFile(barcodePrimerComboFileNames[i][j], temp);
 348                                                 temp << maxFlows << endl;
 349                                                 temp.close();
 350                                         }
 351                                 }
 352                         }
 353                 }
 354
 355                 FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
 356
 357                 ofstream fastaFile;
 358                 if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }
 359
 360                 ifstream flowFile;
 361                 m->openInputFile(flowFileName, flowFile);
 362
 363                 flowFile.seekg(line->start);
 364
 365                 int count = 0;
 366                 bool moreSeqs = 1;
 367
 368                 while(moreSeqs) {
 369
 370                         int success = 1;
 371                         int currentSeqDiffs = 0;
 372                         string trashCode = "";
 373
 374                         flowData.getNext(flowFile);
 375                         flowData.capFlows(maxFlows);
 376
 377                         Sequence currSeq = flowData.getSequence();
 378                         if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
 379                                 success = 0;
 380                                 trashCode += 'l';
 381                         }
 382
 383                         if(minLength > 0 || maxLength > 0){     //screen to see if sequence is above and below a specific number of bases
 384                                 int seqLength = currSeq.getNumBases();
 385                                 if(seqLength < minLength || seqLength > maxLength){
 386                                         success = 0;
 387                                         trashCode += 'l';
 388                                 }
 389                         }
 390
 391                         int primerIndex = 0;
 392                         int barcodeIndex = 0;
 393
 394                         if(barcodes.size() != 0){
 395                                 success = stripBarcode(currSeq, barcodeIndex);
 396                                 if(success > bdiffs)            {       trashCode += 'b';       }
 397                                 else{ currentSeqDiffs += success;  }
 398                         }
 399
 400                         if(numFPrimers != 0){
 401                                 success = stripForward(currSeq, primerIndex);
 402                                 if(success > pdiffs)            {       trashCode += 'f';       }
 403                                 else{ currentSeqDiffs += success;  }
 404                         }
 405
 406                         if (currentSeqDiffs > tdiffs)   {       trashCode += 't';   }
 407
 408                         if(numRPrimers != 0){
 409                                 success = stripReverse(currSeq);
 410                                 if(!success)                            {       trashCode += 'r';       }
 411                         }
 412
 413                         if(trashCode.length() == 0){
 414
 415                                 flowData.printFlows(trimFlowFile);
 416
 417                                 if(fasta)       {       currSeq.printSequence(fastaFile);       }
 418
 419                                 if(allFiles){
 420                                         ofstream output;
 421                                         m->openOutputFileAppend(barcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 422                                         output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 423
 424                                         flowData.printFlows(output);
 425                                         output.close();
 426                                 }
 427                         }
 428                         else{
 429                                 flowData.printFlows(scrapFlowFile, trashCode);
 430                         }
 431
 432                         count++;
 433
 434                         //report progress
 435                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 436
 437 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 438                         unsigned long int pos = flowFile.tellg();
 439
 440                         if ((pos == -1) || (pos >= line->end)) { break; }
 441 #else
 442                         if (flowFile.eof()) { break; }
 443 #endif
 444
 445                 }
 446                 //report progress
 447                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 448
 449                 trimFlowFile.close();
 450                 scrapFlowFile.close();
 451                 flowFile.close();
 452                 if(fasta){      fastaFile.close();      }
 453
 454                 return count;
 455         }
 456         catch(exception& e) {
 457                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 458                 exit(1);
 459         }
 460 }
 461
 462 //***************************************************************************************************************
 463
 464 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 465         try {
 466                 ifstream oligosFile;
 467                 m->openInputFile(oligoFileName, oligosFile);
 468
 469                 string type, oligo, group;
 470
 471                 int indexPrimer = 0;
 472                 int indexBarcode = 0;
 473
 474                 while(!oligosFile.eof()){
 475
 476                         oligosFile >> type; m->gobble(oligosFile);      //get the first column value of the row - is it a comment or a feature we are interested in?
 477
 478                         if(type[0] == '#'){     //igore the line because there's a comment
 479                                 while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       } // get rest of line if there's any crap there
 480                         }
 481                         else{                           //there's a feature we're interested in
 482
 483                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 484
 485                                 oligosFile >> oligo;    //get the DNA sequence for the feature
 486
 487                                 for(int i=0;i<oligo.length();i++){      //make type case insensitive and change any U's to T's
 488                                         oligo[i] = toupper(oligo[i]);
 489                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 490                                 }
 491
 492                                 if(type == "FORWARD"){  //if the feature is a forward primer...
 493                                         group = "";
 494
 495                                         while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
 496                                                 char c = oligosFile.get();
 497                                                 if (c == 10 || c == 13){        break;  }
 498                                                 else if (c == 32 || c == 9){;} //space or tab
 499                                                 else {  group += c;  }
 500                                         }
 501
 502                                         //have we seen this primer already?
 503                                         map<string, int>::iterator itPrimer = primers.find(oligo);
 504                                         if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 505
 506                                         primers[oligo]=indexPrimer; indexPrimer++;
 507                                         primerNameVector.push_back(group);
 508
 509                                 }
 510                                 else if(type == "REVERSE"){
 511                                         Sequence oligoRC("reverse", oligo);
 512                                         oligoRC.reverseComplement();
 513                                         revPrimer.push_back(oligoRC.getUnaligned());
 514                                 }
 515                                 else if(type == "BARCODE"){
 516                                         oligosFile >> group;
 517
 518                                         //check for repeat barcodes
 519                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 520                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 521
 522                                         barcodes[oligo]=indexBarcode; indexBarcode++;
 523                                         barcodeNameVector.push_back(group);
 524                                 }
 525                                 else{
 526                                         m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
 527                                 }
 528                         }
 529
 530                         m->gobble(oligosFile);
 531                 }
 532                 oligosFile.close();
 533
 534                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
 535
 536                 //add in potential combos
 537                 if(barcodeNameVector.size() == 0){
 538                         barcodes[""] = 0;
 539                         barcodeNameVector.push_back("");
 540                 }
 541
 542                 if(primerNameVector.size() == 0){
 543                         primers[""] = 0;
 544                         primerNameVector.push_back("");
 545                 }
 546
 547
 548                 outFlowFileNames.resize(barcodeNameVector.size());
 549                 for(int i=0;i<outFlowFileNames.size();i++){
 550                         outFlowFileNames[i].assign(primerNameVector.size(), "");
 551                 }
 552
 553                 if(allFiles){
 554
 555                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 556                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 557
 558                                         string primerName = primerNameVector[itPrimer->second];
 559                                         string barcodeName = barcodeNameVector[itBar->second];
 560
 561                                         string comboGroupName = "";
 562                                         string fileName = "";
 563
 564                                         if(primerName == ""){
 565                                                 comboGroupName = barcodeNameVector[itBar->second];
 566                                                 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
 567                                         }
 568                                         else{
 569                                                 if(barcodeName == ""){
 570                                                         comboGroupName = primerNameVector[itPrimer->second];
 571                                                 }
 572                                                 else{
 573                                                         comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
 574                                                 }
 575                                                 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
 576                                         }
 577
 578                                         outFlowFileNames[itBar->second][itPrimer->second] = fileName;
 579
 580                                         ofstream temp;
 581                                         m->openOutputFile(fileName, temp);
 582                                         temp.close();
 583                                 }
 584                         }
 585                 }
 586
 587                 numFPrimers = primers.size();
 588                 numRPrimers = revPrimer.size();
 589
 590         }
 591         catch(exception& e) {
 592                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 593                 exit(1);
 594         }
 595 }
 596
 597 //***************************************************************************************************************
 598
 599 int TrimFlowsCommand::stripBarcode(Sequence& seq, int& group){
 600         try {
 601
 602                 string rawSequence = seq.getUnaligned();
 603                 int success = bdiffs + 1;       //guilty until proven innocent
 604
 605                 //can you find the barcode
 606                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 607                         string oligo = it->first;
 608                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 609                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 610                                 break;
 611                         }
 612
 613                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 614                                 group = it->second;
 615                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 616
 617                                 success = 0;
 618                                 break;
 619                         }
 620                 }
 621
 622                 //if you found the barcode or if you don't want to allow for diffs
 623                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 624
 625                 else { //try aligning and see if you can find it
 626
 627                         int maxLength = 0;
 628
 629                         Alignment* alignment;
 630                         if (barcodes.size() > 0) {
 631                                 map<string,int>::iterator it=barcodes.begin();
 632
 633                                 for(it;it!=barcodes.end();it++){
 634                                         if(it->first.length() > maxLength){
 635                                                 maxLength = it->first.length();
 636                                         }
 637                                 }
 638                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
 639
 640                         }else{ alignment = NULL; }
 641
 642                         //can you find the barcode
 643                         int minDiff = 1e6;
 644                         int minCount = 1;
 645                         int minGroup = -1;
 646                         int minPos = 0;
 647
 648                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 649                                 string oligo = it->first;
 650                                 //                              int length = oligo.length();
 651
 652                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 653                                         success = bdiffs + 10;
 654                                         break;
 655                                 }
 656
 657                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 658                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 659                                 oligo = alignment->getSeqAAln();
 660                                 string temp = alignment->getSeqBAln();
 661
 662                                 int alnLength = oligo.length();
 663
 664                                 for(int i=oligo.length()-1;i>=0;i--){
 665                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 666                                 }
 667                                 oligo = oligo.substr(0,alnLength);
 668                                 temp = temp.substr(0,alnLength);
 669
 670                                 int numDiff = countDiffs(oligo, temp);
 671
 672                                 if(numDiff < minDiff){
 673                                         minDiff = numDiff;
 674                                         minCount = 1;
 675                                         minGroup = it->second;
 676                                         minPos = 0;
 677                                         for(int i=0;i<alnLength;i++){
 678                                                 if(temp[i] != '-'){
 679                                                         minPos++;
 680                                                 }
 681                                         }
 682                                 }
 683                                 else if(numDiff == minDiff){
 684                                         minCount++;
 685                                 }
 686
 687                         }
 688
 689                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
 690                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
 691                         else{                                                                                                   //use the best match
 692                                 group = minGroup;
 693                                 seq.setUnaligned(rawSequence.substr(minPos));
 694                                 success = minDiff;
 695                         }
 696
 697                         if (alignment != NULL) {  delete alignment;  }
 698
 699                 }
 700
 701                 return success;
 702
 703         }
 704         catch(exception& e) {
 705                 m->errorOut(e, "TrimFlowsCommand", "stripBarcode");
 706                 exit(1);
 707         }
 708
 709 }
 710
 711 //***************************************************************************************************************
 712
 713 int TrimFlowsCommand::stripForward(Sequence& seq, int& group){
 714         try {
 715
 716                 string rawSequence = seq.getUnaligned();
 717                 int success = pdiffs + 1;       //guilty until proven innocent
 718
 719                 //can you find the primer
 720                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 721                         string oligo = it->first;
 722                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
 723                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 724                                 break;
 725                         }
 726
 727                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 728                                 group = it->second;
 729                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 730                                 success = 0;
 731                                 break;
 732                         }
 733                 }
 734
 735                 //if you found the barcode or if you don't want to allow for diffs
 736                 if ((pdiffs == 0) || (success == 0)) {  return success;  }
 737
 738                 else { //try aligning and see if you can find it
 739
 740                         int maxLength = 0;
 741
 742                         Alignment* alignment;
 743                         if (primers.size() > 0) {
 744                                 map<string,int>::iterator it=primers.begin();
 745
 746                                 for(it;it!=primers.end();it++){
 747                                         if(it->first.length() > maxLength){
 748                                                 maxLength = it->first.length();
 749                                         }
 750                                 }
 751                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
 752
 753                         }else{ alignment = NULL; }
 754
 755                         //can you find the barcode
 756                         int minDiff = 1e6;
 757                         int minCount = 1;
 758                         int minGroup = -1;
 759                         int minPos = 0;
 760
 761                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 762                                 string oligo = it->first;
 763                                 //                              int length = oligo.length();
 764
 765                                 if(rawSequence.length() < maxLength){
 766                                         success = pdiffs + 100;
 767                                         break;
 768                                 }
 769
 770                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 771                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 772                                 oligo = alignment->getSeqAAln();
 773                                 string temp = alignment->getSeqBAln();
 774
 775                                 int alnLength = oligo.length();
 776
 777                                 for(int i=oligo.length()-1;i>=0;i--){
 778                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 779                                 }
 780                                 oligo = oligo.substr(0,alnLength);
 781                                 temp = temp.substr(0,alnLength);
 782
 783                                 int numDiff = countDiffs(oligo, temp);
 784
 785                                 if(numDiff < minDiff){
 786                                         minDiff = numDiff;
 787                                         minCount = 1;
 788                                         minGroup = it->second;
 789                                         minPos = 0;
 790                                         for(int i=0;i<alnLength;i++){
 791                                                 if(temp[i] != '-'){
 792                                                         minPos++;
 793                                                 }
 794                                         }
 795                                 }
 796                                 else if(numDiff == minDiff){
 797                                         minCount++;
 798                                 }
 799
 800                         }
 801
 802                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
 803                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
 804                         else{                                                                                                   //use the best match
 805                                 group = minGroup;
 806                                 seq.setUnaligned(rawSequence.substr(minPos));
 807                                 success = minDiff;
 808                         }
 809
 810                         if (alignment != NULL) {  delete alignment;  }
 811
 812                 }
 813
 814                 return success;
 815
 816         }
 817         catch(exception& e) {
 818                 m->errorOut(e, "TrimFlowsCommand", "stripForward");
 819                 exit(1);
 820         }
 821 }
 822
 823 //***************************************************************************************************************
 824
 825 bool TrimFlowsCommand::stripReverse(Sequence& seq){
 826         try {
 827
 828                 string rawSequence = seq.getUnaligned();
 829                 bool success = 0;       //guilty until proven innocent
 830
 831                 for(int i=0;i<numRPrimers;i++){
 832                         string oligo = revPrimer[i];
 833
 834                         if(rawSequence.length() < oligo.length()){
 835                                 success = 0;
 836                                 break;
 837                         }
 838
 839                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 840                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 841                                 success = 1;
 842                                 break;
 843                         }
 844                 }
 845
 846                 return success;
 847
 848         }
 849         catch(exception& e) {
 850                 m->errorOut(e, "TrimFlowsCommand", "stripReverse");
 851                 exit(1);
 852         }
 853 }
 854
 855
 856 //***************************************************************************************************************
 857
 858 bool TrimFlowsCommand::compareDNASeq(string oligo, string seq){
 859         try {
 860                 bool success = 1;
 861                 int length = oligo.length();
 862
 863                 for(int i=0;i<length;i++){
 864
 865                         if(oligo[i] != seq[i]){
 866                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 867                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 868                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 869                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 870                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 871                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 872                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 873                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 874                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 875                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 876                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 877                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 878
 879                                 if(success == 0)        {       break;   }
 880                         }
 881                         else{
 882                                 success = 1;
 883                         }
 884                 }
 885
 886                 return success;
 887         }
 888         catch(exception& e) {
 889                 m->errorOut(e, "TrimFlowsCommand", "compareDNASeq");
 890                 exit(1);
 891         }
 892
 893 }
 894
 895 //***************************************************************************************************************
 896
 897 int TrimFlowsCommand::countDiffs(string oligo, string seq){
 898         try {
 899
 900                 int length = oligo.length();
 901                 int countDiffs = 0;
 902
 903                 for(int i=0;i<length;i++){
 904
 905                         if(oligo[i] != seq[i]){
 906                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
 907                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
 908                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
 909                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
 910                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
 911                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
 912                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
 913                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
 914                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 915                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 916                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
 917                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
 918                         }
 919
 920                 }
 921
 922                 return countDiffs;
 923         }
 924         catch(exception& e) {
 925                 m->errorOut(e, "TrimFlowsCommand", "countDiffs");
 926                 exit(1);
 927         }
 928
 929 }
 930
 931 /**************************************************************************************************/
 932
 933 vector<unsigned long int> TrimFlowsCommand::getFlowFileBreaks() {
 934
 935         try{
 936
 937                 vector<unsigned long int> filePos;
 938                 filePos.push_back(0);
 939
 940                 FILE * pFile;
 941                 unsigned long int size;
 942
 943                 //get num bytes in file
 944                 pFile = fopen (flowFileName.c_str(),"rb");
 945                 if (pFile==NULL) perror ("Error opening file");
 946                 else{
 947                         fseek (pFile, 0, SEEK_END);
 948                         size=ftell (pFile);
 949                         fclose (pFile);
 950                 }
 951
 952                 //estimate file breaks
 953                 unsigned long int chunkSize = 0;
 954                 chunkSize = size / processors;
 955
 956                 //file too small to divide by processors
 957                 if (chunkSize == 0)  {  processors = 1; filePos.push_back(size); return filePos;        }
 958
 959                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 960                 for (int i = 0; i < processors; i++) {
 961                         unsigned long int spot = (i+1) * chunkSize;
 962
 963                         ifstream in;
 964                         m->openInputFile(flowFileName, in);
 965                         in.seekg(spot);
 966
 967                         string dummy = m->getline(in);
 968
 969                         //there was not another sequence before the end of the file
 970                         unsigned long int sanityPos = in.tellg();
 971
 972 //                      if (sanityPos == -1) {  break;  }
 973 //                      else {  filePos.push_back(newSpot);  }
 974                         if (sanityPos == -1) {  break;  }
 975                         else {  filePos.push_back(sanityPos);  }
 976
 977                         in.close();
 978                 }
 979
 980                 //save end pos
 981                 filePos.push_back(size);
 982
 983                 //sanity check filePos
 984                 for (int i = 0; i < (filePos.size()-1); i++) {
 985                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 986                 }
 987
 988                 ifstream in;
 989                 m->openInputFile(flowFileName, in);
 990                 in >> numFlows;
 991                 m->gobble(in);
 992                 unsigned long int spot = in.tellg();
 993                 filePos[0] = spot;
 994                 in.close();
 995
 996                 processors = (filePos.size() - 1);
 997
 998                 return filePos;
 999         }
1000         catch(exception& e) {
1001                 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
1002                 exit(1);
1003         }
1004 }
1005
1006 /**************************************************************************************************/
1007
1008 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
1009
1010         try {
1011 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1012                 int process = 1;
1013                 int exitCommand = 1;
1014                 processIDS.clear();
1015
1016                 //loop through and create all the processes you want
1017                 while (process != processors) {
1018                         int pid = fork();
1019
1020                         if (pid > 0) {
1021                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1022                                 process++;
1023                         }else if (pid == 0){
1024
1025                                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
1026                                 if(allFiles){
1027                                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
1028                                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
1029                                                         tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
1030                                                         ofstream temp;
1031                                                         m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
1032                                                         temp.close();
1033
1034                                                 }
1035                                         }
1036                                 }
1037                                 driverCreateTrim(flowFileName,
1038                                                                  (trimFlowFileName + toString(getpid()) + ".temp"),
1039                                                                  (scrapFlowFileName + toString(getpid()) + ".temp"),
1040                                                                  (fastaFileName + toString(getpid()) + ".temp"),
1041                                                                  tempBarcodePrimerComboFileNames, lines[process]);
1042
1043                                 exit(0);
1044                         }else {
1045                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1046                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1047                                 exit(0);
1048                         }
1049                 }
1050
1051                 //parent do my part
1052                 ofstream temp;
1053                 m->openOutputFile(trimFlowFileName, temp);
1054                 temp.close();
1055
1056                 m->openOutputFile(scrapFlowFileName, temp);
1057                 temp.close();
1058
1059                 if(fasta){
1060                         m->openOutputFile(fastaFileName, temp);
1061                         temp.close();
1062                 }
1063
1064                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
1065
1066                 //force parent to wait until all the processes are done
1067                 for (int i=0;i<processIDS.size();i++) {
1068                         int temp = processIDS[i];
1069                         wait(&temp);
1070                 }
1071
1072                 //append files
1073                 m->mothurOutEndLine();
1074                 for(int i=0;i<processIDS.size();i++){
1075
1076                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
1077
1078                         m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
1079                         remove((trimFlowFileName + toString(processIDS[i]) + ".temp").c_str());
1080 //                      m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
1081
1082                         m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
1083                         remove((scrapFlowFileName + toString(processIDS[i]) + ".temp").c_str());
1084 //                      m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
1085
1086                         if(fasta){
1087                                 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
1088                                 remove((fastaFileName + toString(processIDS[i]) + ".temp").c_str());
1089 //                              m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
1090                         }
1091                         if(allFiles){
1092                                 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
1093                                         for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
1094                                                 m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
1095                                                 remove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
1096                                         }
1097                                 }
1098                         }
1099                 }
1100
1101                 return exitCommand;
1102 #endif
1103         }
1104         catch(exception& e) {
1105                 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
1106                 exit(1);
1107         }
1108 }
1109
1110 //***************************************************************************************************************