trimseqscommand.cpp

   1 /*
   2  *  trimseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/6/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "trimseqscommand.h"
  11
  12 //***************************************************************************************************************
  13
  14 TrimSeqsCommand::TrimSeqsCommand(string option){
  15         try {
  16
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
  25                                                                         "qthreshold", "qaverage", "allfiles", "qtrim", "outputdir","inputdir"};
  26
  27                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  28
  29                         OptionParser parser(option);
  30                         map<string,string> parameters = parser.getParameters();
  31
  32                         ValidParameters validParameter;
  33                         map<string,string>::iterator it;
  34
  35                         //check to make sure all parameters are valid for command
  36                         for (it = parameters.begin(); it != parameters.end(); it++) {
  37                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  38                         }
  39
  40                         //if the user changes the input directory command factory will send this info to us in the output parameter
  41                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  42                         if (inputDir == "not found"){   inputDir = "";          }
  43                         else {
  44                                 string path;
  45                                 it = parameters.find("fasta");
  46                                 //user has given a template file
  47                                 if(it != parameters.end()){
  48                                         path = hasPath(it->second);
  49                                         //if the user has not given a path then, add inputdir. else leave path alone.
  50                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  51                                 }
  52
  53                                 it = parameters.find("oligos");
  54                                 //user has given a template file
  55                                 if(it != parameters.end()){
  56                                         path = hasPath(it->second);
  57                                         //if the user has not given a path then, add inputdir. else leave path alone.
  58                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
  59                                 }
  60
  61                                 it = parameters.find("qfile");
  62                                 //user has given a template file
  63                                 if(it != parameters.end()){
  64                                         path = hasPath(it->second);
  65                                         //if the user has not given a path then, add inputdir. else leave path alone.
  66                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
  67                                 }
  68                         }
  69
  70
  71                         //check for required parameters
  72                         fastaFile = validParameter.validFile(parameters, "fasta", true);
  73                         if (fastaFile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
  74                         else if (fastaFile == "not open") { abort = true; }
  75
  76                         //if the user changes the output directory command factory will send this info to us in the output parameter
  77                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  78                                 outputDir = "";
  79                                 outputDir += hasPath(fastaFile); //if user entered a file with a path then preserve it
  80                         }
  81
  82                         //check for optional parameter and set defaults
  83                         // ...at some point should added some additional type checking...
  84                         string temp;
  85                         temp = validParameter.validFile(parameters, "flip", false);
  86                         if (temp == "not found"){       flip = 0;       }
  87                         else if(isTrue(temp))   {       flip = 1;       }
  88
  89                         temp = validParameter.validFile(parameters, "oligos", true);
  90                         if (temp == "not found"){       oligoFile = "";         }
  91                         else if(temp == "not open"){    abort = true;   }
  92                         else                                    {       oligoFile = temp;               }
  93
  94                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
  95                         convert(temp, maxAmbig);
  96
  97                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
  98                         convert(temp, maxHomoP);
  99
 100                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
 101                         convert(temp, minLength);
 102
 103                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
 104                         convert(temp, maxLength);
 105
 106                         temp = validParameter.validFile(parameters, "qfile", true);
 107                         if (temp == "not found")        {       qFileName = "";         }
 108                         else if(temp == "not open")     {       abort = 0;              }
 109                         else                                            {       qFileName = temp;       }
 110
 111                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 112                         convert(temp, qThreshold);
 113
 114                         temp = validParameter.validFile(parameters, "qtrim", false);    if (temp == "not found") { temp = "F"; }
 115                         qtrim = isTrue(temp);
 116
 117                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 118                         convert(temp, qAverage);
 119
 120                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 121                         allFiles = isTrue(temp);
 122
 123                         if(allFiles && oligoFile == ""){
 124                                 mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); mothurOutEndLine();
 125                         }
 126                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 127                                 mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); mothurOutEndLine();
 128                                 qAverage=0;
 129                                 qThreshold=0;
 130                         }
 131                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 132                                 mothurOut("You didn't set any options... quiting command."); mothurOutEndLine();
 133                                 abort = true;
 134                         }
 135                 }
 136
 137         }
 138         catch(exception& e) {
 139                 errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 140                 exit(1);
 141         }
 142 }
 143 //**********************************************************************************************************************
 144
 145 void TrimSeqsCommand::help(){
 146         try {
 147                 mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 148                 mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, qtrim and allfiles.\n");
 149                 mothurOut("The fasta parameter is required.\n");
 150                 mothurOut("The flip parameter .... The default is 0.\n");
 151                 mothurOut("The oligos parameter .... The default is "".\n");
 152                 mothurOut("The maxambig parameter .... The default is -1.\n");
 153                 mothurOut("The maxhomop parameter .... The default is 0.\n");
 154                 mothurOut("The minlength parameter .... The default is 0.\n");
 155                 mothurOut("The maxlength parameter .... The default is 0.\n");
 156                 mothurOut("The qfile parameter .....\n");
 157                 mothurOut("The qthreshold parameter .... The default is 0.\n");
 158                 mothurOut("The qaverage parameter .... The default is 0.\n");
 159                 mothurOut("The allfiles parameter .... The default is F.\n");
 160                 mothurOut("The qtrim parameter .... The default is F.\n");
 161                 mothurOut("The trim.seqs command should be in the following format: \n");
 162                 mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
 163                 mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 164                 mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 165                 mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
 166                 mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 167
 168         }
 169         catch(exception& e) {
 170                 errorOut(e, "TrimSeqsCommand", "help");
 171                 exit(1);
 172         }
 173 }
 174
 175
 176 //***************************************************************************************************************
 177
 178 TrimSeqsCommand::~TrimSeqsCommand(){    /*      do nothing      */      }
 179
 180 //***************************************************************************************************************
 181
 182 int TrimSeqsCommand::execute(){
 183         try{
 184
 185                 if (abort == true) { return 0; }
 186
 187                 ifstream inFASTA;
 188                 openInputFile(fastaFile, inFASTA);
 189
 190                 ofstream outFASTA;
 191                 string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
 192                 openOutputFile(trimSeqFile, outFASTA);
 193
 194                 ofstream outGroups;
 195                 vector<ofstream*> fastaFileNames;
 196                 if(oligoFile != ""){
 197                         string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
 198                         openOutputFile(groupFile, outGroups);
 199                         getOligos(fastaFileNames);
 200                 }
 201
 202                 ofstream scrapFASTA;
 203                 string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
 204                 openOutputFile(scrapSeqFile, scrapFASTA);
 205
 206                 ifstream qFile;
 207                 if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
 208
 209                 bool success;
 210
 211                 while(!inFASTA.eof()){
 212                         Sequence currSeq(inFASTA);
 213                         string origSeq = currSeq.getUnaligned();
 214                         if (origSeq != "") {
 215                                 int group;
 216                                 string trashCode = "";
 217
 218                                 if(qFileName != ""){
 219                                         if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
 220                                         else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
 221                                         if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) {
 222                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 223                                         }
 224                                         if(!success)                    {       trashCode += 'q';                                                               }
 225                                 }
 226
 227                                 if(barcodes.size() != 0){
 228                                         success = stripBarcode(currSeq, group);
 229                                         if(!success){   trashCode += 'b';       }
 230                                 }
 231
 232                                 if(numFPrimers != 0){
 233                                         success = stripForward(currSeq);
 234                                         if(!success){   trashCode += 'f';       }
 235                                 }
 236
 237                                 if(numRPrimers != 0){
 238                                         success = stripReverse(currSeq);
 239                                         if(!success){   trashCode += 'r';       }
 240                                 }
 241                                 if(minLength > 0 || maxLength > 0){
 242                                         success = cullLength(currSeq);
 243                                         if(!success){   trashCode += 'l'; }
 244                                 }
 245                                 if(maxHomoP > 0){
 246                                         success = cullHomoP(currSeq);
 247                                         if(!success){   trashCode += 'h';       }
 248                                 }
 249                                 if(maxAmbig != -1){
 250                                         success = cullAmbigs(currSeq);
 251                                         if(!success){   trashCode += 'n';       }
 252                                 }
 253
 254                                 if(flip){       currSeq.reverseComplement();    }               // should go last
 255
 256                                 if(trashCode.length() == 0){
 257                                         currSeq.setAligned(currSeq.getUnaligned());  //this is because of a modification we made to the sequence class to fix a bug.  all seqs have an aligned version, which is the version that gets printed.
 258                                         currSeq.printSequence(outFASTA);
 259                                         if(barcodes.size() != 0){
 260                                                 outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
 261
 262                                                 if(allFiles){
 263                                                         currSeq.printSequence(*fastaFileNames[group]);
 264                                                 }
 265                                         }
 266                                 }
 267                                 else{
 268                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 269                                         currSeq.setUnaligned(origSeq);
 270                                         currSeq.printSequence(scrapFASTA);
 271                                 }
 272                         }
 273                         gobble(inFASTA);
 274                 }
 275                 inFASTA.close();
 276                 outFASTA.close();
 277                 scrapFASTA.close();
 278                 outGroups.close();
 279                 if(qFileName != "")     {       qFile.close();  }
 280
 281                 for(int i=0;i<fastaFileNames.size();i++){
 282                         fastaFileNames[i]->close();
 283                         delete fastaFileNames[i];
 284                 }
 285
 286                 for(int i=0;i<fastaFileNames.size();i++){
 287                         string seqName;
 288                         openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
 289                         ofstream outGroups;
 290                         openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
 291
 292                         while(!inFASTA.eof()){
 293                                 if(inFASTA.get() == '>'){
 294                                         inFASTA >> seqName;
 295                                         outGroups << seqName << '\t' << groupVector[i] << endl;
 296                                 }
 297                                 while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 298                         }
 299                         outGroups.close();
 300                         inFASTA.close();
 301                 }
 302
 303
 304                 return 0;
 305         }
 306         catch(exception& e) {
 307                 errorOut(e, "TrimSeqsCommand", "execute");
 308                 exit(1);
 309         }
 310 }
 311
 312 //***************************************************************************************************************
 313
 314 void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
 315         try {
 316                 ifstream inOligos;
 317                 openInputFile(oligoFile, inOligos);
 318
 319                 ofstream test;
 320
 321                 string type, oligo, group;
 322                 int index=0;
 323
 324                 while(!inOligos.eof()){
 325                         inOligos >> type;
 326
 327                         if(type[0] == '#'){
 328                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 329                         }
 330                         else{
 331                                 inOligos >> oligo;
 332
 333                                 for(int i=0;i<oligo.length();i++){
 334                                         oligo[i] = toupper(oligo[i]);
 335                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 336                                 }
 337
 338                                 if(type == "forward"){
 339                                         forPrimer.push_back(oligo);
 340                                 }
 341                                 else if(type == "reverse"){
 342                                         Sequence oligoRC("reverse", oligo);
 343                                         oligoRC.reverseComplement();
 344                                         revPrimer.push_back(oligoRC.getUnaligned());
 345                                 }
 346                                 else if(type == "barcode"){
 347                                         inOligos >> group;
 348                                         barcodes[oligo]=index++;
 349                                         groupVector.push_back(group);
 350
 351                                         if(allFiles){
 352                                                 outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
 353                                         }
 354                                 }
 355                         }
 356                 }
 357
 358                 inOligos.close();
 359
 360                 numFPrimers = forPrimer.size();
 361                 numRPrimers = revPrimer.size();
 362
 363         }
 364         catch(exception& e) {
 365                 errorOut(e, "TrimSeqsCommand", "getOligos");
 366                 exit(1);
 367         }
 368
 369 }
 370
 371 //***************************************************************************************************************
 372
 373 bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 374         try {
 375                 string rawSequence = seq.getUnaligned();
 376                 bool success = 0;       //guilty until proven innocent
 377
 378                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 379                         string oligo = it->first;
 380                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 381                                 success = 0;
 382                                 break;
 383                         }
 384
 385                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 386                                 group = it->second;
 387                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 388                                 success = 1;
 389                                 break;
 390                         }
 391                 }
 392                 return success;
 393
 394         }
 395         catch(exception& e) {
 396                 errorOut(e, "TrimSeqsCommand", "stripBarcode");
 397                 exit(1);
 398         }
 399
 400 }
 401
 402 //***************************************************************************************************************
 403
 404 bool TrimSeqsCommand::stripForward(Sequence& seq){
 405         try {
 406                 string rawSequence = seq.getUnaligned();
 407                 bool success = 0;       //guilty until proven innocent
 408
 409                 for(int i=0;i<numFPrimers;i++){
 410                         string oligo = forPrimer[i];
 411
 412                         if(rawSequence.length() < oligo.length()){
 413                                 success = 0;
 414                                 break;
 415                         }
 416
 417                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 418                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 419                                 success = 1;
 420                                 break;
 421                         }
 422                 }
 423
 424                 return success;
 425
 426         }
 427         catch(exception& e) {
 428                 errorOut(e, "TrimSeqsCommand", "stripForward");
 429                 exit(1);
 430         }
 431 }
 432
 433 //***************************************************************************************************************
 434
 435 bool TrimSeqsCommand::stripReverse(Sequence& seq){
 436         try {
 437                 string rawSequence = seq.getUnaligned();
 438                 bool success = 0;       //guilty until proven innocent
 439
 440                 for(int i=0;i<numRPrimers;i++){
 441                         string oligo = revPrimer[i];
 442
 443                         if(rawSequence.length() < oligo.length()){
 444                                 success = 0;
 445                                 break;
 446                         }
 447
 448                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 449                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 450                                 success = 1;
 451                                 break;
 452                         }
 453                 }
 454                 return success;
 455
 456         }
 457         catch(exception& e) {
 458                 errorOut(e, "TrimSeqsCommand", "stripReverse");
 459                 exit(1);
 460         }
 461 }
 462
 463 //***************************************************************************************************************
 464
 465 bool TrimSeqsCommand::cullLength(Sequence& seq){
 466         try {
 467
 468                 int length = seq.getNumBases();
 469                 bool success = 0;       //guilty until proven innocent
 470
 471                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
 472                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
 473                 else                                                                                            {       success = 0;    }
 474
 475                 return success;
 476
 477         }
 478         catch(exception& e) {
 479                 errorOut(e, "TrimSeqsCommand", "cullLength");
 480                 exit(1);
 481         }
 482
 483 }
 484
 485 //***************************************************************************************************************
 486
 487 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
 488         try {
 489                 int longHomoP = seq.getLongHomoPolymer();
 490                 bool success = 0;       //guilty until proven innocent
 491
 492                 if(longHomoP <= maxHomoP){      success = 1;    }
 493                 else                                    {       success = 0;    }
 494
 495                 return success;
 496         }
 497         catch(exception& e) {
 498                 errorOut(e, "TrimSeqsCommand", "cullHomoP");
 499                 exit(1);
 500         }
 501
 502 }
 503
 504 //***************************************************************************************************************
 505
 506 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
 507         try {
 508                 int numNs = seq.getAmbigBases();
 509                 bool success = 0;       //guilty until proven innocent
 510
 511                 if(numNs <= maxAmbig)   {       success = 1;    }
 512                 else                                    {       success = 0;    }
 513
 514                 return success;
 515         }
 516         catch(exception& e) {
 517                 errorOut(e, "TrimSeqsCommand", "cullAmbigs");
 518                 exit(1);
 519         }
 520
 521 }
 522
 523 //***************************************************************************************************************
 524
 525 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 526         try {
 527                 bool success = 1;
 528                 int length = oligo.length();
 529
 530                 for(int i=0;i<length;i++){
 531
 532                         if(oligo[i] != seq[i]){
 533                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 534                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 535                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 536                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 537                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 538                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 539                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 540                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 541                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 542                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 543                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 544                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 545
 546                                 if(success == 0)        {       break;  }
 547                         }
 548                         else{
 549                                 success = 1;
 550                         }
 551                 }
 552
 553                 return success;
 554         }
 555         catch(exception& e) {
 556                 errorOut(e, "TrimSeqsCommand", "compareDNASeq");
 557                 exit(1);
 558         }
 559
 560 }
 561
 562 //***************************************************************************************************************
 563
 564 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
 565         try {
 566                 string rawSequence = seq.getUnaligned();
 567                 int seqLength = rawSequence.length();
 568                 string name;
 569
 570                 qFile >> name;
 571                 if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine();       }  }
 572                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
 573
 574                 int score;
 575                 int end = seqLength;
 576
 577                 for(int i=0;i<seqLength;i++){
 578                         qFile >> score;
 579
 580                         if(score <= qThreshold){
 581                                 end = i;
 582                                 break;
 583                         }
 584                 }
 585                 for(int i=end+1;i<seqLength;i++){
 586                         qFile >> score;
 587                 }
 588
 589                 seq.setUnaligned(rawSequence.substr(0,end));
 590
 591                 return 1;
 592         }
 593         catch(exception& e) {
 594                 errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
 595                 exit(1);
 596         }
 597 }
 598
 599 //***************************************************************************************************************
 600
 601 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
 602         try {
 603                 string rawSequence = seq.getUnaligned();
 604                 int seqLength = seq.getNumBases();
 605                 bool success = 0;       //guilty until proven innocent
 606                 string name;
 607
 608                 qFile >> name;
 609                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); mothurOutEndLine();       } }
 610
 611                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
 612
 613                 float score;
 614                 float average = 0;
 615
 616                 for(int i=0;i<seqLength;i++){
 617                         qFile >> score;
 618                         average += score;
 619                 }
 620                 average /= seqLength;
 621
 622                 if(average >= qAverage) {       success = 1;    }
 623                 else                                    {       success = 0;    }
 624
 625                 return success;
 626         }
 627         catch(exception& e) {
 628                 errorOut(e, "TrimSeqsCommand", "cullQualAverage");
 629                 exit(1);
 630         }
 631 }
 632
 633 //***************************************************************************************************************