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
  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") {
 140                                 flowFileName = m->getFlowFile();
 141                                 if (flowFileName != "") {  m->mothurOut("Using " + flowFileName + " as input file for the flow parameter."); m->mothurOutEndLine(); }
 142                                 else {
 143                                         m->mothurOut("No valid current flow file. You must provide a flow file."); m->mothurOutEndLine();
 144                                         abort = true;
 145                                 }
 146                         }else if (flowFileName == "not open") { flowFileName = ""; abort = true; }
 147
 148                         //if the user changes the output directory command factory will send this info to us in the output parameter
 149                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 150                                 outputDir = "";
 151                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 152                         }
 153
 154
 155                         //check for optional parameter and set defaults
 156                         // ...at some point should added some additional type checking...
 157
 158                         string temp;
 159                         temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "360"; }
 160                         convert(temp, minFlows);
 161
 162                         temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "720"; }
 163                         convert(temp, maxFlows);
 164
 165
 166                         temp = validParameter.validFile(parameters, "oligos", true);
 167                         if (temp == "not found")        {       oligoFileName = "";             }
 168                         else if(temp == "not open")     {       abort = true;                   }
 169                         else                                            {       oligoFileName = temp;   }
 170
 171                         temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
 172                         else if(m->isTrue(temp))        {       fasta = 1;      }
 173
 174                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
 175                         convert(temp, maxHomoP);
 176
 177                         temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
 178                         convert(temp, signal);
 179
 180                         temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
 181                         convert(temp, noise);
 182
 183                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found"){       temp = "0";             }
 184                         convert(temp, minLength);
 185
 186                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found"){       temp = "0";             }
 187                         convert(temp, maxLength);
 188
 189                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
 190                         convert(temp, bdiffs);
 191
 192                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
 193                         convert(temp, pdiffs);
 194
 195                         temp = validParameter.validFile(parameters, "tdiffs", false);
 196                         if (temp == "not found"){ int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 197                         convert(temp, tdiffs);
 198                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 199
 200                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found"){ temp = "T";           }
 201                         allFiles = m->isTrue(temp);
 202
 203                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 204                         m->setProcessors(temp);
 205                         convert(temp, processors);
 206
 207                         flowOrder = validParameter.validFile(parameters, "order", false);
 208                         if (flowOrder == "not found"){ flowOrder = "TACG";              }
 209                         else if(flowOrder.length() != 4){
 210                                 m->mothurOut("The value of the order option must be four bases long\n");
 211                         }
 212
 213                         if(oligoFileName == ""){        allFiles = 0;           }
 214
 215                         numFPrimers = 0;
 216                         numRPrimers = 0;
 217                 }
 218
 219         }
 220         catch(exception& e) {
 221                 m->errorOut(e, "TrimFlowsCommand", "TrimSeqsCommand");
 222                 exit(1);
 223         }
 224 }
 225
 226 //***************************************************************************************************************
 227
 228 int TrimFlowsCommand::execute(){
 229         try{
 230
 231                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 232
 233                 string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
 234                 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
 235
 236                 string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap.flow";
 237                 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 238
 239                 string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.fasta";
 240                 if(fasta){
 241                         outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
 242                 }
 243
 244                 vector<unsigned long int> flowFilePos = getFlowFileBreaks();
 245                 for (int i = 0; i < (flowFilePos.size()-1); i++) {
 246                         lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
 247                 }
 248
 249                 vector<vector<string> > barcodePrimerComboFileNames;
 250                 if(oligoFileName != ""){
 251                         getOligos(barcodePrimerComboFileNames);
 252                 }
 253
 254 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 255                 if(processors == 1){
 256                         driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 257                 }else{
 258                         createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
 259                 }
 260 #else
 261                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 262 #endif
 263
 264                 if (m->control_pressed) {  return 0; }
 265
 266                 string flowFilesFileName;
 267                 ofstream output;
 268
 269                 if(allFiles){
 270
 271                         flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
 272                         m->openOutputFile(flowFilesFileName, output);
 273
 274                         for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 275                                 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 276
 277                                         FILE * pFile;
 278                                         unsigned long int size;
 279
 280                                         //get num bytes in file
 281                                         pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
 282                                         if (pFile==NULL) perror ("Error opening file");
 283                                         else{
 284                                                 fseek (pFile, 0, SEEK_END);
 285                                                 size=ftell (pFile);
 286                                                 fclose (pFile);
 287                                         }
 288
 289                                         if(size < 10){
 290                                                 remove(barcodePrimerComboFileNames[i][j].c_str());
 291                                         }
 292                                         else{
 293                                                 output << barcodePrimerComboFileNames[i][j] << endl;
 294                                         }
 295                                 }
 296                         }
 297                         output.close();
 298                 }
 299                 else{
 300                         flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
 301                         m->openOutputFile(flowFilesFileName, output);
 302
 303                         output << trimFlowFileName << endl;
 304
 305                         output.close();
 306                 }
 307                 outputTypes["flow.files"].push_back(flowFilesFileName);
 308                 outputNames.push_back(flowFileName);
 309
 310                 //set fasta file as new current fastafile
 311                 string current = "";
 312                 itTypes = outputTypes.find("fasta");
 313                 if (itTypes != outputTypes.end()) {
 314                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 315                 }
 316
 317                 m->mothurOutEndLine();
 318                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 319                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 320                 m->mothurOutEndLine();
 321
 322                 return 0;
 323         }
 324         catch(exception& e) {
 325                 m->errorOut(e, "TrimSeqsCommand", "execute");
 326                 exit(1);
 327         }
 328 }
 329
 330 //***************************************************************************************************************
 331
 332 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames, linePair* line){
 333
 334         try {
 335
 336                 ofstream trimFlowFile;
 337                 m->openOutputFile(trimFlowFileName, trimFlowFile);
 338                 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 339
 340                 ofstream scrapFlowFile;
 341                 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
 342                 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
 343
 344                 if(line->start == 4){
 345                         scrapFlowFile << maxFlows << endl;
 346                         trimFlowFile << maxFlows << endl;
 347                         if(allFiles){
 348                                 for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 349                                         for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 350                                                 //                              barcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
 351                                                 ofstream temp;
 352                                                 m->openOutputFile(barcodePrimerComboFileNames[i][j], temp);
 353                                                 temp << maxFlows << endl;
 354                                                 temp.close();
 355                                         }
 356                                 }
 357                         }
 358                 }
 359
 360                 FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
 361
 362                 ofstream fastaFile;
 363                 if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }
 364
 365                 ifstream flowFile;
 366                 m->openInputFile(flowFileName, flowFile);
 367
 368                 flowFile.seekg(line->start);
 369
 370                 int count = 0;
 371                 bool moreSeqs = 1;
 372
 373                 while(moreSeqs) {
 374
 375                         int success = 1;
 376                         int currentSeqDiffs = 0;
 377                         string trashCode = "";
 378
 379                         flowData.getNext(flowFile);
 380                         flowData.capFlows(maxFlows);
 381
 382                         Sequence currSeq = flowData.getSequence();
 383                         if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
 384                                 success = 0;
 385                                 trashCode += 'l';
 386                         }
 387
 388                         if(minLength > 0 || maxLength > 0){     //screen to see if sequence is above and below a specific number of bases
 389                                 int seqLength = currSeq.getNumBases();
 390                                 if(seqLength < minLength || seqLength > maxLength){
 391                                         success = 0;
 392                                         trashCode += 'l';
 393                                 }
 394                         }
 395
 396                         int primerIndex = 0;
 397                         int barcodeIndex = 0;
 398
 399                         if(barcodes.size() != 0){
 400                                 success = stripBarcode(currSeq, barcodeIndex);
 401                                 if(success > bdiffs)            {       trashCode += 'b';       }
 402                                 else{ currentSeqDiffs += success;  }
 403                         }
 404
 405                         if(numFPrimers != 0){
 406                                 success = stripForward(currSeq, primerIndex);
 407                                 if(success > pdiffs)            {       trashCode += 'f';       }
 408                                 else{ currentSeqDiffs += success;  }
 409                         }
 410
 411                         if (currentSeqDiffs > tdiffs)   {       trashCode += 't';   }
 412
 413                         if(numRPrimers != 0){
 414                                 success = stripReverse(currSeq);
 415                                 if(!success)                            {       trashCode += 'r';       }
 416                         }
 417
 418                         if(trashCode.length() == 0){
 419
 420                                 flowData.printFlows(trimFlowFile);
 421
 422                                 if(fasta)       {       currSeq.printSequence(fastaFile);       }
 423
 424                                 if(allFiles){
 425                                         ofstream output;
 426                                         m->openOutputFileAppend(barcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 427                                         output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 428
 429                                         flowData.printFlows(output);
 430                                         output.close();
 431                                 }
 432                         }
 433                         else{
 434                                 flowData.printFlows(scrapFlowFile, trashCode);
 435                         }
 436
 437                         count++;
 438
 439                         //report progress
 440                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 441
 442 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 443                         unsigned long int pos = flowFile.tellg();
 444
 445                         if ((pos == -1) || (pos >= line->end)) { break; }
 446 #else
 447                         if (flowFile.eof()) { break; }
 448 #endif
 449
 450                 }
 451                 //report progress
 452                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 453
 454                 trimFlowFile.close();
 455                 scrapFlowFile.close();
 456                 flowFile.close();
 457                 if(fasta){      fastaFile.close();      }
 458
 459                 return count;
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 463                 exit(1);
 464         }
 465 }
 466
 467 //***************************************************************************************************************
 468
 469 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 470         try {
 471                 ifstream oligosFile;
 472                 m->openInputFile(oligoFileName, oligosFile);
 473
 474                 string type, oligo, group;
 475
 476                 int indexPrimer = 0;
 477                 int indexBarcode = 0;
 478
 479                 while(!oligosFile.eof()){
 480
 481                         oligosFile >> type; m->gobble(oligosFile);      //get the first column value of the row - is it a comment or a feature we are interested in?
 482
 483                         if(type[0] == '#'){     //igore the line because there's a comment
 484                                 while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       } // get rest of line if there's any crap there
 485                         }
 486                         else{                           //there's a feature we're interested in
 487
 488                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 489
 490                                 oligosFile >> oligo;    //get the DNA sequence for the feature
 491
 492                                 for(int i=0;i<oligo.length();i++){      //make type case insensitive and change any U's to T's
 493                                         oligo[i] = toupper(oligo[i]);
 494                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 495                                 }
 496
 497                                 if(type == "FORWARD"){  //if the feature is a forward primer...
 498                                         group = "";
 499
 500                                         while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
 501                                                 char c = oligosFile.get();
 502                                                 if (c == 10 || c == 13){        break;  }
 503                                                 else if (c == 32 || c == 9){;} //space or tab
 504                                                 else {  group += c;  }
 505                                         }
 506
 507                                         //have we seen this primer already?
 508                                         map<string, int>::iterator itPrimer = primers.find(oligo);
 509                                         if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 510
 511                                         primers[oligo]=indexPrimer; indexPrimer++;
 512                                         primerNameVector.push_back(group);
 513
 514                                 }
 515                                 else if(type == "REVERSE"){
 516                                         Sequence oligoRC("reverse", oligo);
 517                                         oligoRC.reverseComplement();
 518                                         revPrimer.push_back(oligoRC.getUnaligned());
 519                                 }
 520                                 else if(type == "BARCODE"){
 521                                         oligosFile >> group;
 522
 523                                         //check for repeat barcodes
 524                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 525                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 526
 527                                         barcodes[oligo]=indexBarcode; indexBarcode++;
 528                                         barcodeNameVector.push_back(group);
 529                                 }
 530                                 else{
 531                                         m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
 532                                 }
 533                         }
 534
 535                         m->gobble(oligosFile);
 536                 }
 537                 oligosFile.close();
 538
 539                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
 540
 541                 //add in potential combos
 542                 if(barcodeNameVector.size() == 0){
 543                         barcodes[""] = 0;
 544                         barcodeNameVector.push_back("");
 545                 }
 546
 547                 if(primerNameVector.size() == 0){
 548                         primers[""] = 0;
 549                         primerNameVector.push_back("");
 550                 }
 551
 552
 553                 outFlowFileNames.resize(barcodeNameVector.size());
 554                 for(int i=0;i<outFlowFileNames.size();i++){
 555                         outFlowFileNames[i].assign(primerNameVector.size(), "");
 556                 }
 557
 558                 if(allFiles){
 559
 560                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 561                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 562
 563                                         string primerName = primerNameVector[itPrimer->second];
 564                                         string barcodeName = barcodeNameVector[itBar->second];
 565
 566                                         string comboGroupName = "";
 567                                         string fileName = "";
 568
 569                                         if(primerName == ""){
 570                                                 comboGroupName = barcodeNameVector[itBar->second];
 571                                                 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
 572                                         }
 573                                         else{
 574                                                 if(barcodeName == ""){
 575                                                         comboGroupName = primerNameVector[itPrimer->second];
 576                                                 }
 577                                                 else{
 578                                                         comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
 579                                                 }
 580                                                 fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
 581                                         }
 582
 583                                         outputNames.push_back(fileName);
 584                                         outputTypes["flow"].push_back(fileName);
 585                                         outFlowFileNames[itBar->second][itPrimer->second] = fileName;
 586
 587                                         ofstream temp;
 588                                         m->openOutputFile(fileName, temp);
 589                                         temp.close();
 590                                 }
 591                         }
 592                 }
 593
 594                 numFPrimers = primers.size();
 595                 numRPrimers = revPrimer.size();
 596
 597         }
 598         catch(exception& e) {
 599                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 600                 exit(1);
 601         }
 602 }
 603
 604 //***************************************************************************************************************
 605
 606 int TrimFlowsCommand::stripBarcode(Sequence& seq, int& group){
 607         try {
 608
 609                 string rawSequence = seq.getUnaligned();
 610                 int success = bdiffs + 1;       //guilty until proven innocent
 611
 612                 //can you find the barcode
 613                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 614                         string oligo = it->first;
 615                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 616                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 617                                 break;
 618                         }
 619
 620                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 621                                 group = it->second;
 622                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 623
 624                                 success = 0;
 625                                 break;
 626                         }
 627                 }
 628
 629                 //if you found the barcode or if you don't want to allow for diffs
 630                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 631
 632                 else { //try aligning and see if you can find it
 633
 634                         int maxLength = 0;
 635
 636                         Alignment* alignment;
 637                         if (barcodes.size() > 0) {
 638                                 map<string,int>::iterator it=barcodes.begin();
 639
 640                                 for(it;it!=barcodes.end();it++){
 641                                         if(it->first.length() > maxLength){
 642                                                 maxLength = it->first.length();
 643                                         }
 644                                 }
 645                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
 646
 647                         }else{ alignment = NULL; }
 648
 649                         //can you find the barcode
 650                         int minDiff = 1e6;
 651                         int minCount = 1;
 652                         int minGroup = -1;
 653                         int minPos = 0;
 654
 655                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 656                                 string oligo = it->first;
 657                                 //                              int length = oligo.length();
 658
 659                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 660                                         success = bdiffs + 10;
 661                                         break;
 662                                 }
 663
 664                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 665                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 666                                 oligo = alignment->getSeqAAln();
 667                                 string temp = alignment->getSeqBAln();
 668
 669                                 int alnLength = oligo.length();
 670
 671                                 for(int i=oligo.length()-1;i>=0;i--){
 672                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 673                                 }
 674                                 oligo = oligo.substr(0,alnLength);
 675                                 temp = temp.substr(0,alnLength);
 676
 677                                 int numDiff = countDiffs(oligo, temp);
 678
 679                                 if(numDiff < minDiff){
 680                                         minDiff = numDiff;
 681                                         minCount = 1;
 682                                         minGroup = it->second;
 683                                         minPos = 0;
 684                                         for(int i=0;i<alnLength;i++){
 685                                                 if(temp[i] != '-'){
 686                                                         minPos++;
 687                                                 }
 688                                         }
 689                                 }
 690                                 else if(numDiff == minDiff){
 691                                         minCount++;
 692                                 }
 693
 694                         }
 695
 696                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
 697                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
 698                         else{                                                                                                   //use the best match
 699                                 group = minGroup;
 700                                 seq.setUnaligned(rawSequence.substr(minPos));
 701                                 success = minDiff;
 702                         }
 703
 704                         if (alignment != NULL) {  delete alignment;  }
 705
 706                 }
 707
 708                 return success;
 709
 710         }
 711         catch(exception& e) {
 712                 m->errorOut(e, "TrimFlowsCommand", "stripBarcode");
 713                 exit(1);
 714         }
 715
 716 }
 717
 718 //***************************************************************************************************************
 719
 720 int TrimFlowsCommand::stripForward(Sequence& seq, int& group){
 721         try {
 722
 723                 string rawSequence = seq.getUnaligned();
 724                 int success = pdiffs + 1;       //guilty until proven innocent
 725
 726                 //can you find the primer
 727                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 728                         string oligo = it->first;
 729                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
 730                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 731                                 break;
 732                         }
 733
 734                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 735                                 group = it->second;
 736                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 737                                 success = 0;
 738                                 break;
 739                         }
 740                 }
 741
 742                 //if you found the barcode or if you don't want to allow for diffs
 743                 if ((pdiffs == 0) || (success == 0)) {  return success;  }
 744
 745                 else { //try aligning and see if you can find it
 746
 747                         int maxLength = 0;
 748
 749                         Alignment* alignment;
 750                         if (primers.size() > 0) {
 751                                 map<string,int>::iterator it=primers.begin();
 752
 753                                 for(it;it!=primers.end();it++){
 754                                         if(it->first.length() > maxLength){
 755                                                 maxLength = it->first.length();
 756                                         }
 757                                 }
 758                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
 759
 760                         }else{ alignment = NULL; }
 761
 762                         //can you find the barcode
 763                         int minDiff = 1e6;
 764                         int minCount = 1;
 765                         int minGroup = -1;
 766                         int minPos = 0;
 767
 768                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 769                                 string oligo = it->first;
 770                                 //                              int length = oligo.length();
 771
 772                                 if(rawSequence.length() < maxLength){
 773                                         success = pdiffs + 100;
 774                                         break;
 775                                 }
 776
 777                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 778                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 779                                 oligo = alignment->getSeqAAln();
 780                                 string temp = alignment->getSeqBAln();
 781
 782                                 int alnLength = oligo.length();
 783
 784                                 for(int i=oligo.length()-1;i>=0;i--){
 785                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 786                                 }
 787                                 oligo = oligo.substr(0,alnLength);
 788                                 temp = temp.substr(0,alnLength);
 789
 790                                 int numDiff = countDiffs(oligo, temp);
 791
 792                                 if(numDiff < minDiff){
 793                                         minDiff = numDiff;
 794                                         minCount = 1;
 795                                         minGroup = it->second;
 796                                         minPos = 0;
 797                                         for(int i=0;i<alnLength;i++){
 798                                                 if(temp[i] != '-'){
 799                                                         minPos++;
 800                                                 }
 801                                         }
 802                                 }
 803                                 else if(numDiff == minDiff){
 804                                         minCount++;
 805                                 }
 806
 807                         }
 808
 809                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
 810                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
 811                         else{                                                                                                   //use the best match
 812                                 group = minGroup;
 813                                 seq.setUnaligned(rawSequence.substr(minPos));
 814                                 success = minDiff;
 815                         }
 816
 817                         if (alignment != NULL) {  delete alignment;  }
 818
 819                 }
 820
 821                 return success;
 822
 823         }
 824         catch(exception& e) {
 825                 m->errorOut(e, "TrimFlowsCommand", "stripForward");
 826                 exit(1);
 827         }
 828 }
 829
 830 //***************************************************************************************************************
 831
 832 bool TrimFlowsCommand::stripReverse(Sequence& seq){
 833         try {
 834
 835                 string rawSequence = seq.getUnaligned();
 836                 bool success = 0;       //guilty until proven innocent
 837
 838                 for(int i=0;i<numRPrimers;i++){
 839                         string oligo = revPrimer[i];
 840
 841                         if(rawSequence.length() < oligo.length()){
 842                                 success = 0;
 843                                 break;
 844                         }
 845
 846                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 847                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 848                                 success = 1;
 849                                 break;
 850                         }
 851                 }
 852
 853                 return success;
 854
 855         }
 856         catch(exception& e) {
 857                 m->errorOut(e, "TrimFlowsCommand", "stripReverse");
 858                 exit(1);
 859         }
 860 }
 861
 862
 863 //***************************************************************************************************************
 864
 865 bool TrimFlowsCommand::compareDNASeq(string oligo, string seq){
 866         try {
 867                 bool success = 1;
 868                 int length = oligo.length();
 869
 870                 for(int i=0;i<length;i++){
 871
 872                         if(oligo[i] != seq[i]){
 873                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 874                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 875                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 876                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 877                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 878                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 879                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 880                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 881                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 882                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 883                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 884                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 885
 886                                 if(success == 0)        {       break;   }
 887                         }
 888                         else{
 889                                 success = 1;
 890                         }
 891                 }
 892
 893                 return success;
 894         }
 895         catch(exception& e) {
 896                 m->errorOut(e, "TrimFlowsCommand", "compareDNASeq");
 897                 exit(1);
 898         }
 899
 900 }
 901
 902 //***************************************************************************************************************
 903
 904 int TrimFlowsCommand::countDiffs(string oligo, string seq){
 905         try {
 906
 907                 int length = oligo.length();
 908                 int countDiffs = 0;
 909
 910                 for(int i=0;i<length;i++){
 911
 912                         if(oligo[i] != seq[i]){
 913                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
 914                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
 915                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
 916                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
 917                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
 918                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
 919                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
 920                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
 921                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 922                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 923                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
 924                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
 925                         }
 926
 927                 }
 928
 929                 return countDiffs;
 930         }
 931         catch(exception& e) {
 932                 m->errorOut(e, "TrimFlowsCommand", "countDiffs");
 933                 exit(1);
 934         }
 935
 936 }
 937
 938 /**************************************************************************************************/
 939
 940 vector<unsigned long int> TrimFlowsCommand::getFlowFileBreaks() {
 941
 942         try{
 943
 944                 vector<unsigned long int> filePos;
 945                 filePos.push_back(0);
 946
 947                 FILE * pFile;
 948                 unsigned long int size;
 949
 950                 //get num bytes in file
 951                 pFile = fopen (flowFileName.c_str(),"rb");
 952                 if (pFile==NULL) perror ("Error opening file");
 953                 else{
 954                         fseek (pFile, 0, SEEK_END);
 955                         size=ftell (pFile);
 956                         fclose (pFile);
 957                 }
 958
 959                 //estimate file breaks
 960                 unsigned long int chunkSize = 0;
 961                 chunkSize = size / processors;
 962
 963                 //file too small to divide by processors
 964                 if (chunkSize == 0)  {  processors = 1; filePos.push_back(size); return filePos;        }
 965
 966                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 967                 for (int i = 0; i < processors; i++) {
 968                         unsigned long int spot = (i+1) * chunkSize;
 969
 970                         ifstream in;
 971                         m->openInputFile(flowFileName, in);
 972                         in.seekg(spot);
 973
 974                         string dummy = m->getline(in);
 975
 976                         //there was not another sequence before the end of the file
 977                         unsigned long int sanityPos = in.tellg();
 978
 979 //                      if (sanityPos == -1) {  break;  }
 980 //                      else {  filePos.push_back(newSpot);  }
 981                         if (sanityPos == -1) {  break;  }
 982                         else {  filePos.push_back(sanityPos);  }
 983
 984                         in.close();
 985                 }
 986
 987                 //save end pos
 988                 filePos.push_back(size);
 989
 990                 //sanity check filePos
 991                 for (int i = 0; i < (filePos.size()-1); i++) {
 992                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 993                 }
 994
 995                 ifstream in;
 996                 m->openInputFile(flowFileName, in);
 997                 in >> numFlows;
 998                 m->gobble(in);
 999                 unsigned long int spot = in.tellg();
1000                 filePos[0] = spot;
1001                 in.close();
1002
1003                 processors = (filePos.size() - 1);
1004
1005                 return filePos;
1006         }
1007         catch(exception& e) {
1008                 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
1009                 exit(1);
1010         }
1011 }
1012
1013 /**************************************************************************************************/
1014
1015 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
1016
1017         try {
1018 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1019                 int process = 1;
1020                 int exitCommand = 1;
1021                 processIDS.clear();
1022
1023                 //loop through and create all the processes you want
1024                 while (process != processors) {
1025                         int pid = fork();
1026
1027                         if (pid > 0) {
1028                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1029                                 process++;
1030                         }else if (pid == 0){
1031
1032                                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
1033                                 if(allFiles){
1034                                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
1035                                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
1036                                                         tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
1037                                                         ofstream temp;
1038                                                         m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
1039                                                         temp.close();
1040
1041                                                 }
1042                                         }
1043                                 }
1044                                 driverCreateTrim(flowFileName,
1045                                                                  (trimFlowFileName + toString(getpid()) + ".temp"),
1046                                                                  (scrapFlowFileName + toString(getpid()) + ".temp"),
1047                                                                  (fastaFileName + toString(getpid()) + ".temp"),
1048                                                                  tempBarcodePrimerComboFileNames, lines[process]);
1049
1050                                 exit(0);
1051                         }else {
1052                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1053                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1054                                 exit(0);
1055                         }
1056                 }
1057
1058                 //parent do my part
1059                 ofstream temp;
1060                 m->openOutputFile(trimFlowFileName, temp);
1061                 temp.close();
1062
1063                 m->openOutputFile(scrapFlowFileName, temp);
1064                 temp.close();
1065
1066                 if(fasta){
1067                         m->openOutputFile(fastaFileName, temp);
1068                         temp.close();
1069                 }
1070
1071                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
1072
1073                 //force parent to wait until all the processes are done
1074                 for (int i=0;i<processIDS.size();i++) {
1075                         int temp = processIDS[i];
1076                         wait(&temp);
1077                 }
1078
1079                 //append files
1080                 m->mothurOutEndLine();
1081                 for(int i=0;i<processIDS.size();i++){
1082
1083                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
1084
1085                         m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
1086                         remove((trimFlowFileName + toString(processIDS[i]) + ".temp").c_str());
1087 //                      m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
1088
1089                         m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
1090                         remove((scrapFlowFileName + toString(processIDS[i]) + ".temp").c_str());
1091 //                      m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
1092
1093                         if(fasta){
1094                                 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
1095                                 remove((fastaFileName + toString(processIDS[i]) + ".temp").c_str());
1096 //                              m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
1097                         }
1098                         if(allFiles){
1099                                 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
1100                                         for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
1101                                                 m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
1102                                                 remove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
1103                                         }
1104                                 }
1105                         }
1106                 }
1107
1108                 return exitCommand;
1109 #endif
1110         }
1111         catch(exception& e) {
1112                 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
1113                 exit(1);
1114         }
1115 }
1116
1117 //***************************************************************************************************************