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\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
  85                 else {
  86
  87                         vector<string> myArray = setParameters();
  88
  89                         OptionParser parser(option);
  90                         map<string,string> parameters = parser.getParameters();
  91
  92                         ValidParameters validParameter;
  93                         map<string,string>::iterator it;
  94
  95                         //check to make sure all parameters are valid for command
  96                         for (it = parameters.begin(); it != parameters.end(); it++) {
  97                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  98                         }
  99
 100                         //initialize outputTypes
 101                         vector<string> tempOutNames;
 102                         outputTypes["flow"] = tempOutNames;
 103                         outputTypes["fasta"] = tempOutNames;
 104
 105                         //if the user changes the input directory command factory will send this info to us in the output parameter
 106                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 107                         if (inputDir == "not found"){   inputDir = "";          }
 108                         else {
 109                                 string path;
 110                                 it = parameters.find("flow");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 116                                 }
 117
 118                                 it = parameters.find("oligos");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 124                                 }
 125
 126
 127 //                              it = parameters.find("group");
 128 //                              //user has given a template file
 129 //                              if(it != parameters.end()){
 130 //                                      path = m->hasPath(it->second);
 131 //                                      //if the user has not given a path then, add inputdir. else leave path alone.
 132 //                                      if (path == "") {       parameters["group"] = inputDir + it->second;            }
 133 //                              }
 134                         }
 135
 136
 137                         //check for required parameters
 138                         flowFileName = validParameter.validFile(parameters, "flow", true);
 139                         if (flowFileName == "not found") { m->mothurOut("flow is a required parameter for the trim.flows command."); m->mothurOutEndLine(); abort = true; }
 140                         else if (flowFileName == "not open") { abort = true; }
 141
 142                         //if the user changes the output directory command factory will send this info to us in the output parameter
 143                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 144                                 outputDir = "";
 145                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 146                         }
 147
 148
 149                         //check for optional parameter and set defaults
 150                         // ...at some point should added some additional type checking...
 151
 152                         string temp;
 153                         temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "360"; }
 154                         convert(temp, minFlows);
 155
 156                         temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "720"; }
 157                         convert(temp, maxFlows);
 158
 159
 160                         temp = validParameter.validFile(parameters, "oligos", true);
 161                         if (temp == "not found")        {       oligoFileName = "";             }
 162                         else if(temp == "not open")     {       abort = true;                   }
 163                         else                                            {       oligoFileName = temp;   }
 164
 165                         temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
 166                         else if(m->isTrue(temp))        {       fasta = 1;      }
 167
 168                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
 169                         convert(temp, maxHomoP);
 170
 171                         temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
 172                         convert(temp, signal);
 173
 174                         temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
 175                         convert(temp, noise);
 176
 177                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found"){       temp = "0";             }
 178                         convert(temp, minLength);
 179
 180                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found"){       temp = "0";             }
 181                         convert(temp, maxLength);
 182
 183                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
 184                         convert(temp, bdiffs);
 185
 186                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
 187                         convert(temp, pdiffs);
 188
 189                         temp = validParameter.validFile(parameters, "tdiffs", false);
 190                         if (temp == "not found"){ int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 191                         convert(temp, tdiffs);
 192                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 193
 194                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found"){ temp = "T";           }
 195                         allFiles = m->isTrue(temp);
 196
 197                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 198                         m->setProcessors(temp);
 199                         convert(temp, processors);
 200
 201                         flowOrder = validParameter.validFile(parameters, "order", false);
 202                         if (flowOrder == "not found"){ flowOrder = "TACG";              }
 203                         else if(flowOrder.length() != 4){
 204                                 m->mothurOut("The value of the order option must be four bases long\n");
 205                         }
 206
 207                         if(oligoFileName == ""){        allFiles = 0;           }
 208
 209                         numFPrimers = 0;
 210                         numRPrimers = 0;
 211                 }
 212
 213         }
 214         catch(exception& e) {
 215                 m->errorOut(e, "TrimFlowsCommand", "TrimSeqsCommand");
 216                 exit(1);
 217         }
 218 }
 219
 220 //***************************************************************************************************************
 221
 222 int TrimFlowsCommand::execute(){
 223         try{
 224
 225                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 226
 227                 string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
 228                 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
 229
 230                 string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap.flow";
 231                 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 232
 233                 string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.fasta";
 234                 if(fasta){
 235                         outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
 236                 }
 237
 238                 vector<unsigned long int> flowFilePos = getFlowFileBreaks();
 239                 for (int i = 0; i < (flowFilePos.size()-1); i++) {
 240                         lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
 241                 }
 242
 243                 vector<vector<string> > barcodePrimerComboFileNames;
 244                 if(oligoFileName != ""){
 245                         getOligos(barcodePrimerComboFileNames);
 246                 }
 247
 248 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 249                 if(processors == 1){
 250                         driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 251                 }else{
 252                         createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
 253                 }
 254 #else
 255                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 256 #endif
 257
 258                 if (m->control_pressed) {  return 0; }
 259
 260                 string flowFilesFileName;
 261                 ofstream output;
 262
 263                 if(allFiles){
 264
 265                         flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
 266                         m->openOutputFile(flowFilesFileName, output);
 267
 268                         for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 269                                 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 270
 271                                         FILE * pFile;
 272                                         unsigned long int size;
 273
 274                                         //get num bytes in file
 275                                         pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
 276                                         if (pFile==NULL) perror ("Error opening file");
 277                                         else{
 278                                                 fseek (pFile, 0, SEEK_END);
 279                                                 size=ftell (pFile);
 280                                                 fclose (pFile);
 281                                         }
 282
 283                                         if(size < 10){
 284                                                 remove(barcodePrimerComboFileNames[i][j].c_str());
 285                                         }
 286                                         else{
 287                                                 output << barcodePrimerComboFileNames[i][j] << endl;
 288                                         }
 289                                 }
 290                         }
 291                         output.close();
 292                 }
 293                 else{
 294                         flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
 295                         m->openOutputFile(flowFilesFileName, output);
 296
 297                         output << trimFlowFileName << endl;
 298
 299                         output.close();
 300                 }
 301                 outputTypes["flow.files"].push_back(flowFilesFileName);
 302                 outputNames.push_back(flowFileName);
 303
 304                 //set fasta file as new current fastafile
 305                 string current = "";
 306                 itTypes = outputTypes.find("fasta");
 307                 if (itTypes != outputTypes.end()) {
 308                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 309                 }
 310
 311                 m->mothurOutEndLine();
 312                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 313                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 314                 m->mothurOutEndLine();
 315
 316                 return 0;
 317         }
 318         catch(exception& e) {
 319                 m->errorOut(e, "TrimSeqsCommand", "execute");
 320                 exit(1);
 321         }
 322 }
 323
 324 //***************************************************************************************************************
 325
 326 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames, linePair* line){
 327
 328         try {
 329
 330                 ofstream trimFlowFile;
 331                 m->openOutputFile(trimFlowFileName, trimFlowFile);
 332                 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 333
 334                 ofstream scrapFlowFile;
 335                 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
 336                 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
 337
 338                 if(line->start == 4){
 339                         scrapFlowFile << maxFlows << endl;
 340                         trimFlowFile << maxFlows << endl;
 341                         if(allFiles){
 342                                 for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 343                                         for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 344                                                 //                              barcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
 345                                                 ofstream temp;
 346                                                 m->openOutputFile(barcodePrimerComboFileNames[i][j], temp);
 347                                                 temp << maxFlows << endl;
 348                                                 temp.close();
 349                                         }
 350                                 }
 351                         }
 352                 }
 353
 354                 FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
 355
 356                 ofstream fastaFile;
 357                 if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }
 358
 359                 ifstream flowFile;
 360                 m->openInputFile(flowFileName, flowFile);
 361
 362                 flowFile.seekg(line->start);
 363
 364                 int count = 0;
 365                 bool moreSeqs = 1;
 366
 367                 while(moreSeqs) {
 368
 369                         int success = 1;
 370                         int currentSeqDiffs = 0;
 371                         string trashCode = "";
 372
 373                         flowData.getNext(flowFile);
 374                         flowData.capFlows(maxFlows);
 375
 376                         Sequence currSeq = flowData.getSequence();
 377                         if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
 378                                 success = 0;
 379                                 trashCode += 'l';
 380                         }
 381
 382                         if(minLength > 0 || maxLength > 0){     //screen to see if sequence is above and below a specific number of bases
 383                                 int seqLength = currSeq.getNumBases();
 384                                 if(seqLength < minLength || seqLength > maxLength){
 385                                         success = 0;
 386                                         trashCode += 'l';
 387                                 }
 388                         }
 389
 390                         int primerIndex = 0;
 391                         int barcodeIndex = 0;
 392
 393                         if(barcodes.size() != 0){
 394                                 success = stripBarcode(currSeq, barcodeIndex);
 395                                 if(success > bdiffs)            {       trashCode += 'b';       }
 396                                 else{ currentSeqDiffs += success;  }
 397                         }
 398
 399                         if(numFPrimers != 0){
 400                                 success = stripForward(currSeq, primerIndex);
 401                                 if(success > pdiffs)            {       trashCode += 'f';       }
 402                                 else{ currentSeqDiffs += success;  }
 403                         }
 404
 405                         if (currentSeqDiffs > tdiffs)   {       trashCode += 't';   }
 406
 407                         if(numRPrimers != 0){
 408                                 success = stripReverse(currSeq);
 409                                 if(!success)                            {       trashCode += 'r';       }
 410                         }
 411
 412                         if(trashCode.length() == 0){
 413
 414                                 flowData.printFlows(trimFlowFile);
 415
 416                                 if(fasta)       {       currSeq.printSequence(fastaFile);       }
 417
 418                                 if(allFiles){
 419                                         ofstream output;
 420                                         m->openOutputFileAppend(barcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 421                                         output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 422
 423                                         flowData.printFlows(output);
 424                                         output.close();
 425                                 }
 426                         }
 427                         else{
 428                                 flowData.printFlows(scrapFlowFile, trashCode);
 429                         }
 430
 431                         count++;
 432
 433                         //report progress
 434                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 435
 436 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 437                         unsigned long int pos = flowFile.tellg();
 438
 439                         if ((pos == -1) || (pos >= line->end)) { break; }
 440 #else
 441                         if (flowFile.eof()) { break; }
 442 #endif
 443
 444                 }
 445                 //report progress
 446                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 447
 448                 trimFlowFile.close();
 449                 scrapFlowFile.close();
 450                 flowFile.close();
 451                 if(fasta){      fastaFile.close();      }
 452
 453                 return count;
 454         }
 455         catch(exception& e) {
 456                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 457                 exit(1);
 458         }
 459 }
 460
 461 //***************************************************************************************************************
 462
 463 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 464         try {
 465                 ifstream oligosFile;
 466                 m->openInputFile(oligoFileName, oligosFile);
 467
 468                 string type, oligo, group;
 469
 470                 int indexPrimer = 0;
 471                 int indexBarcode = 0;
 472
 473                 while(!oligosFile.eof()){
 474
 475                         oligosFile >> type; m->gobble(oligosFile);      //get the first column value of the row - is it a comment or a feature we are interested in?
 476
 477                         if(type[0] == '#'){     //igore the line because there's a comment
 478                                 while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       } // get rest of line if there's any crap there
 479                         }
 480                         else{                           //there's a feature we're interested in
 481
 482                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 483
 484                                 oligosFile >> oligo;    //get the DNA sequence for the feature
 485
 486                                 for(int i=0;i<oligo.length();i++){      //make type case insensitive and change any U's to T's
 487                                         oligo[i] = toupper(oligo[i]);
 488                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 489                                 }
 490
 491                                 if(type == "FORWARD"){  //if the feature is a forward primer...
 492                                         group = "";
 493
 494                                         while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
 495                                                 char c = oligosFile.get();
 496                                                 if (c == 10 || c == 13){        break;  }
 497                                                 else if (c == 32 || c == 9){;} //space or tab
 498                                                 else {  group += c;  }
 499                                         }
 500
 501                                         //have we seen this primer already?
 502                                         map<string, int>::iterator itPrimer = primers.find(oligo);
 503                                         if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 504
 505                                         primers[oligo]=indexPrimer; indexPrimer++;
 506                                         primerNameVector.push_back(group);
 507
 508                                 }
 509                                 else if(type == "REVERSE"){
 510                                         Sequence oligoRC("reverse", oligo);
 511                                         oligoRC.reverseComplement();
 512                                         revPrimer.push_back(oligoRC.getUnaligned());
 513                                 }
 514                                 else if(type == "BARCODE"){
 515                                         oligosFile >> group;
 516
 517                                         //check for repeat barcodes
 518                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 519                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 520
 521                                         barcodes[oligo]=indexBarcode; indexBarcode++;
 522                                         barcodeNameVector.push_back(group);
 523                                 }
 524                                 else{
 525                                         m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
 526                                 }
 527                         }
 528
 529                         m->gobble(oligosFile);
 530                 }
 531                 oligosFile.close();
 532
 533                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
 534
 535                 //add in potential combos
 536                 if(barcodeNameVector.size() == 0){
 537                         barcodes[""] = 0;
 538                         barcodeNameVector.push_back("");
 539                 }
 540
 541                 if(primerNameVector.size() == 0){
 542                         primers[""] = 0;
 543                         primerNameVector.push_back("");
 544                 }
 545
 546
 547                 outFlowFileNames.resize(barcodeNameVector.size());
 548                 for(int i=0;i<outFlowFileNames.size();i++){
 549                         outFlowFileNames[i].assign(primerNameVector.size(), "");
 550                 }
 551
 552                 if(allFiles){
 553
 554                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 555                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 556
 557                                         string primerName = primerNameVector[itPrimer->second];
 558                                         string barcodeName = barcodeNameVector[itBar->second];
 559
 560                                         string comboGroupName = "";
 561                                         string fileName = "";
 562
 563                                         if(primerName == ""){
 564                                                 comboGroupName = barcodeNameVector[itBar->second];
 565                                                 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
 566                                         }
 567                                         else{
 568                                                 if(barcodeName == ""){
 569                                                         comboGroupName = primerNameVector[itPrimer->second];
 570                                                 }
 571                                                 else{
 572                                                         comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
 573                                                 }
 574                                                 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
 575                                         }
 576
 577                                         outputNames.push_back(fileName);
 578                                         outputTypes["flow"].push_back(fileName);
 579                                         outFlowFileNames[itBar->second][itPrimer->second] = fileName;
 580
 581                                         ofstream temp;
 582                                         m->openOutputFile(fileName, temp);
 583                                         temp.close();
 584                                 }
 585                         }
 586                 }
 587
 588                 numFPrimers = primers.size();
 589                 numRPrimers = revPrimer.size();
 590
 591         }
 592         catch(exception& e) {
 593                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 594                 exit(1);
 595         }
 596 }
 597
 598 //***************************************************************************************************************
 599
 600 int TrimFlowsCommand::stripBarcode(Sequence& seq, int& group){
 601         try {
 602
 603                 string rawSequence = seq.getUnaligned();
 604                 int success = bdiffs + 1;       //guilty until proven innocent
 605
 606                 //can you find the barcode
 607                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 608                         string oligo = it->first;
 609                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 610                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 611                                 break;
 612                         }
 613
 614                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 615                                 group = it->second;
 616                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 617
 618                                 success = 0;
 619                                 break;
 620                         }
 621                 }
 622
 623                 //if you found the barcode or if you don't want to allow for diffs
 624                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 625
 626                 else { //try aligning and see if you can find it
 627
 628                         int maxLength = 0;
 629
 630                         Alignment* alignment;
 631                         if (barcodes.size() > 0) {
 632                                 map<string,int>::iterator it=barcodes.begin();
 633
 634                                 for(it;it!=barcodes.end();it++){
 635                                         if(it->first.length() > maxLength){
 636                                                 maxLength = it->first.length();
 637                                         }
 638                                 }
 639                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
 640
 641                         }else{ alignment = NULL; }
 642
 643                         //can you find the barcode
 644                         int minDiff = 1e6;
 645                         int minCount = 1;
 646                         int minGroup = -1;
 647                         int minPos = 0;
 648
 649                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 650                                 string oligo = it->first;
 651                                 //                              int length = oligo.length();
 652
 653                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 654                                         success = bdiffs + 10;
 655                                         break;
 656                                 }
 657
 658                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 659                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 660                                 oligo = alignment->getSeqAAln();
 661                                 string temp = alignment->getSeqBAln();
 662
 663                                 int alnLength = oligo.length();
 664
 665                                 for(int i=oligo.length()-1;i>=0;i--){
 666                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 667                                 }
 668                                 oligo = oligo.substr(0,alnLength);
 669                                 temp = temp.substr(0,alnLength);
 670
 671                                 int numDiff = countDiffs(oligo, temp);
 672
 673                                 if(numDiff < minDiff){
 674                                         minDiff = numDiff;
 675                                         minCount = 1;
 676                                         minGroup = it->second;
 677                                         minPos = 0;
 678                                         for(int i=0;i<alnLength;i++){
 679                                                 if(temp[i] != '-'){
 680                                                         minPos++;
 681                                                 }
 682                                         }
 683                                 }
 684                                 else if(numDiff == minDiff){
 685                                         minCount++;
 686                                 }
 687
 688                         }
 689
 690                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
 691                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
 692                         else{                                                                                                   //use the best match
 693                                 group = minGroup;
 694                                 seq.setUnaligned(rawSequence.substr(minPos));
 695                                 success = minDiff;
 696                         }
 697
 698                         if (alignment != NULL) {  delete alignment;  }
 699
 700                 }
 701
 702                 return success;
 703
 704         }
 705         catch(exception& e) {
 706                 m->errorOut(e, "TrimFlowsCommand", "stripBarcode");
 707                 exit(1);
 708         }
 709
 710 }
 711
 712 //***************************************************************************************************************
 713
 714 int TrimFlowsCommand::stripForward(Sequence& seq, int& group){
 715         try {
 716
 717                 string rawSequence = seq.getUnaligned();
 718                 int success = pdiffs + 1;       //guilty until proven innocent
 719
 720                 //can you find the primer
 721                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 722                         string oligo = it->first;
 723                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
 724                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 725                                 break;
 726                         }
 727
 728                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 729                                 group = it->second;
 730                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 731                                 success = 0;
 732                                 break;
 733                         }
 734                 }
 735
 736                 //if you found the barcode or if you don't want to allow for diffs
 737                 if ((pdiffs == 0) || (success == 0)) {  return success;  }
 738
 739                 else { //try aligning and see if you can find it
 740
 741                         int maxLength = 0;
 742
 743                         Alignment* alignment;
 744                         if (primers.size() > 0) {
 745                                 map<string,int>::iterator it=primers.begin();
 746
 747                                 for(it;it!=primers.end();it++){
 748                                         if(it->first.length() > maxLength){
 749                                                 maxLength = it->first.length();
 750                                         }
 751                                 }
 752                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
 753
 754                         }else{ alignment = NULL; }
 755
 756                         //can you find the barcode
 757                         int minDiff = 1e6;
 758                         int minCount = 1;
 759                         int minGroup = -1;
 760                         int minPos = 0;
 761
 762                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 763                                 string oligo = it->first;
 764                                 //                              int length = oligo.length();
 765
 766                                 if(rawSequence.length() < maxLength){
 767                                         success = pdiffs + 100;
 768                                         break;
 769                                 }
 770
 771                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 772                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 773                                 oligo = alignment->getSeqAAln();
 774                                 string temp = alignment->getSeqBAln();
 775
 776                                 int alnLength = oligo.length();
 777
 778                                 for(int i=oligo.length()-1;i>=0;i--){
 779                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 780                                 }
 781                                 oligo = oligo.substr(0,alnLength);
 782                                 temp = temp.substr(0,alnLength);
 783
 784                                 int numDiff = countDiffs(oligo, temp);
 785
 786                                 if(numDiff < minDiff){
 787                                         minDiff = numDiff;
 788                                         minCount = 1;
 789                                         minGroup = it->second;
 790                                         minPos = 0;
 791                                         for(int i=0;i<alnLength;i++){
 792                                                 if(temp[i] != '-'){
 793                                                         minPos++;
 794                                                 }
 795                                         }
 796                                 }
 797                                 else if(numDiff == minDiff){
 798                                         minCount++;
 799                                 }
 800
 801                         }
 802
 803                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
 804                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
 805                         else{                                                                                                   //use the best match
 806                                 group = minGroup;
 807                                 seq.setUnaligned(rawSequence.substr(minPos));
 808                                 success = minDiff;
 809                         }
 810
 811                         if (alignment != NULL) {  delete alignment;  }
 812
 813                 }
 814
 815                 return success;
 816
 817         }
 818         catch(exception& e) {
 819                 m->errorOut(e, "TrimFlowsCommand", "stripForward");
 820                 exit(1);
 821         }
 822 }
 823
 824 //***************************************************************************************************************
 825
 826 bool TrimFlowsCommand::stripReverse(Sequence& seq){
 827         try {
 828
 829                 string rawSequence = seq.getUnaligned();
 830                 bool success = 0;       //guilty until proven innocent
 831
 832                 for(int i=0;i<numRPrimers;i++){
 833                         string oligo = revPrimer[i];
 834
 835                         if(rawSequence.length() < oligo.length()){
 836                                 success = 0;
 837                                 break;
 838                         }
 839
 840                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 841                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 842                                 success = 1;
 843                                 break;
 844                         }
 845                 }
 846
 847                 return success;
 848
 849         }
 850         catch(exception& e) {
 851                 m->errorOut(e, "TrimFlowsCommand", "stripReverse");
 852                 exit(1);
 853         }
 854 }
 855
 856
 857 //***************************************************************************************************************
 858
 859 bool TrimFlowsCommand::compareDNASeq(string oligo, string seq){
 860         try {
 861                 bool success = 1;
 862                 int length = oligo.length();
 863
 864                 for(int i=0;i<length;i++){
 865
 866                         if(oligo[i] != seq[i]){
 867                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 868                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 869                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 870                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 871                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 872                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 873                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 874                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 875                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 876                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 877                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 878                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 879
 880                                 if(success == 0)        {       break;   }
 881                         }
 882                         else{
 883                                 success = 1;
 884                         }
 885                 }
 886
 887                 return success;
 888         }
 889         catch(exception& e) {
 890                 m->errorOut(e, "TrimFlowsCommand", "compareDNASeq");
 891                 exit(1);
 892         }
 893
 894 }
 895
 896 //***************************************************************************************************************
 897
 898 int TrimFlowsCommand::countDiffs(string oligo, string seq){
 899         try {
 900
 901                 int length = oligo.length();
 902                 int countDiffs = 0;
 903
 904                 for(int i=0;i<length;i++){
 905
 906                         if(oligo[i] != seq[i]){
 907                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
 908                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
 909                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
 910                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
 911                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
 912                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
 913                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
 914                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
 915                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 916                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 917                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
 918                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
 919                         }
 920
 921                 }
 922
 923                 return countDiffs;
 924         }
 925         catch(exception& e) {
 926                 m->errorOut(e, "TrimFlowsCommand", "countDiffs");
 927                 exit(1);
 928         }
 929
 930 }
 931
 932 /**************************************************************************************************/
 933
 934 vector<unsigned long int> TrimFlowsCommand::getFlowFileBreaks() {
 935
 936         try{
 937
 938                 vector<unsigned long int> filePos;
 939                 filePos.push_back(0);
 940
 941                 FILE * pFile;
 942                 unsigned long int size;
 943
 944                 //get num bytes in file
 945                 pFile = fopen (flowFileName.c_str(),"rb");
 946                 if (pFile==NULL) perror ("Error opening file");
 947                 else{
 948                         fseek (pFile, 0, SEEK_END);
 949                         size=ftell (pFile);
 950                         fclose (pFile);
 951                 }
 952
 953                 //estimate file breaks
 954                 unsigned long int chunkSize = 0;
 955                 chunkSize = size / processors;
 956
 957                 //file too small to divide by processors
 958                 if (chunkSize == 0)  {  processors = 1; filePos.push_back(size); return filePos;        }
 959
 960                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 961                 for (int i = 0; i < processors; i++) {
 962                         unsigned long int spot = (i+1) * chunkSize;
 963
 964                         ifstream in;
 965                         m->openInputFile(flowFileName, in);
 966                         in.seekg(spot);
 967
 968                         string dummy = m->getline(in);
 969
 970                         //there was not another sequence before the end of the file
 971                         unsigned long int sanityPos = in.tellg();
 972
 973 //                      if (sanityPos == -1) {  break;  }
 974 //                      else {  filePos.push_back(newSpot);  }
 975                         if (sanityPos == -1) {  break;  }
 976                         else {  filePos.push_back(sanityPos);  }
 977
 978                         in.close();
 979                 }
 980
 981                 //save end pos
 982                 filePos.push_back(size);
 983
 984                 //sanity check filePos
 985                 for (int i = 0; i < (filePos.size()-1); i++) {
 986                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 987                 }
 988
 989                 ifstream in;
 990                 m->openInputFile(flowFileName, in);
 991                 in >> numFlows;
 992                 m->gobble(in);
 993                 unsigned long int spot = in.tellg();
 994                 filePos[0] = spot;
 995                 in.close();
 996
 997                 processors = (filePos.size() - 1);
 998
 999                 return filePos;
1000         }
1001         catch(exception& e) {
1002                 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
1003                 exit(1);
1004         }
1005 }
1006
1007 /**************************************************************************************************/
1008
1009 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
1010
1011         try {
1012 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1013                 int process = 1;
1014                 int exitCommand = 1;
1015                 processIDS.clear();
1016
1017                 //loop through and create all the processes you want
1018                 while (process != processors) {
1019                         int pid = fork();
1020
1021                         if (pid > 0) {
1022                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1023                                 process++;
1024                         }else if (pid == 0){
1025
1026                                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
1027                                 if(allFiles){
1028                                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
1029                                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
1030                                                         tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
1031                                                         ofstream temp;
1032                                                         m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
1033                                                         temp.close();
1034
1035                                                 }
1036                                         }
1037                                 }
1038                                 driverCreateTrim(flowFileName,
1039                                                                  (trimFlowFileName + toString(getpid()) + ".temp"),
1040                                                                  (scrapFlowFileName + toString(getpid()) + ".temp"),
1041                                                                  (fastaFileName + toString(getpid()) + ".temp"),
1042                                                                  tempBarcodePrimerComboFileNames, lines[process]);
1043
1044                                 exit(0);
1045                         }else {
1046                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1047                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1048                                 exit(0);
1049                         }
1050                 }
1051
1052                 //parent do my part
1053                 ofstream temp;
1054                 m->openOutputFile(trimFlowFileName, temp);
1055                 temp.close();
1056
1057                 m->openOutputFile(scrapFlowFileName, temp);
1058                 temp.close();
1059
1060                 if(fasta){
1061                         m->openOutputFile(fastaFileName, temp);
1062                         temp.close();
1063                 }
1064
1065                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
1066
1067                 //force parent to wait until all the processes are done
1068                 for (int i=0;i<processIDS.size();i++) {
1069                         int temp = processIDS[i];
1070                         wait(&temp);
1071                 }
1072
1073                 //append files
1074                 m->mothurOutEndLine();
1075                 for(int i=0;i<processIDS.size();i++){
1076
1077                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
1078
1079                         m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
1080                         remove((trimFlowFileName + toString(processIDS[i]) + ".temp").c_str());
1081 //                      m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
1082
1083                         m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
1084                         remove((scrapFlowFileName + toString(processIDS[i]) + ".temp").c_str());
1085 //                      m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
1086
1087                         if(fasta){
1088                                 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
1089                                 remove((fastaFileName + toString(processIDS[i]) + ".temp").c_str());
1090 //                              m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
1091                         }
1092                         if(allFiles){
1093                                 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
1094                                         for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
1095                                                 m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
1096                                                 remove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
1097                                         }
1098                                 }
1099                         }
1100                 }
1101
1102                 return exitCommand;
1103 #endif
1104         }
1105         catch(exception& e) {
1106                 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
1107                 exit(1);
1108         }
1109 }
1110
1111 //***************************************************************************************************************