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 = true;           }
 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                 numFPrimers = 0;  //this needs to be initialized
 188                 numRPrimers = 0;
 189
 190                 ifstream inFASTA;
 191                 openInputFile(fastaFile, inFASTA);
 192
 193                 ofstream outFASTA;
 194                 string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
 195                 openOutputFile(trimSeqFile, outFASTA);
 196
 197                 ofstream outGroups;
 198                 vector<ofstream*> fastaFileNames;
 199                 if(oligoFile != ""){
 200                         string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
 201                         openOutputFile(groupFile, outGroups);
 202                         getOligos(fastaFileNames);
 203                 }
 204
 205                 ofstream scrapFASTA;
 206                 string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
 207                 openOutputFile(scrapSeqFile, scrapFASTA);
 208
 209                 ifstream qFile;
 210                 if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
 211
 212                 bool success;
 213
 214                 while(!inFASTA.eof()){
 215                         Sequence currSeq(inFASTA);
 216
 217                         string origSeq = currSeq.getUnaligned();
 218                         if (origSeq != "") {
 219                                 int group;
 220                                 string trashCode = "";
 221
 222                                 if(qFileName != ""){
 223                                         if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
 224                                         else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
 225                                         if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) {
 226                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 227                                         }
 228                                         if(!success)                    {       trashCode += 'q';                                                               }
 229                                 }
 230
 231                                 if(barcodes.size() != 0){
 232                                         success = stripBarcode(currSeq, group);
 233                                         if(!success){   trashCode += 'b';       }
 234                                 }
 235
 236                                 if(numFPrimers != 0){
 237                                         success = stripForward(currSeq);
 238                                         if(!success){   trashCode += 'f';       }
 239                                 }
 240
 241                                 if(numRPrimers != 0){
 242                                         success = stripReverse(currSeq);
 243                                         if(!success){   trashCode += 'r';       }
 244                                 }
 245
 246                                 if(minLength > 0 || maxLength > 0){
 247                                         success = cullLength(currSeq);
 248                                         if(!success){   trashCode += 'l'; }
 249                                 }
 250                                 if(maxHomoP > 0){
 251                                         success = cullHomoP(currSeq);
 252                                         if(!success){   trashCode += 'h';       }
 253                                 }
 254                                 if(maxAmbig != -1){
 255                                         success = cullAmbigs(currSeq);
 256                                         if(!success){   trashCode += 'n';       }
 257                                 }
 258
 259                                 if(flip){       currSeq.reverseComplement();    }               // should go last
 260
 261                                 if(trashCode.length() == 0){
 262                                         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.
 263                                         currSeq.printSequence(outFASTA);
 264                                         if(barcodes.size() != 0){
 265                                                 outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
 266
 267                                                 if(allFiles){
 268                                                         currSeq.printSequence(*fastaFileNames[group]);
 269                                                 }
 270                                         }
 271                                 }
 272                                 else{
 273                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 274                                         currSeq.setUnaligned(origSeq);
 275                                         currSeq.printSequence(scrapFASTA);
 276                                 }
 277                         }
 278                         gobble(inFASTA);
 279                 }
 280                 inFASTA.close();
 281                 outFASTA.close();
 282                 scrapFASTA.close();
 283                 outGroups.close();
 284                 if(qFileName != "")     {       qFile.close();  }
 285
 286                 for(int i=0;i<fastaFileNames.size();i++){
 287                         fastaFileNames[i]->close();
 288                         delete fastaFileNames[i];
 289                 }
 290
 291                 for(int i=0;i<fastaFileNames.size();i++){
 292                         string seqName;
 293                         openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
 294                         ofstream outGroups;
 295                         openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
 296
 297                         while(!inFASTA.eof()){
 298                                 if(inFASTA.get() == '>'){
 299                                         inFASTA >> seqName;
 300                                         outGroups << seqName << '\t' << groupVector[i] << endl;
 301                                 }
 302                                 while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 303                         }
 304                         outGroups.close();
 305                         inFASTA.close();
 306                 }
 307
 308                 return 0;
 309         }
 310         catch(exception& e) {
 311                 errorOut(e, "TrimSeqsCommand", "execute");
 312                 exit(1);
 313         }
 314 }
 315
 316 //***************************************************************************************************************
 317
 318 void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
 319         try {
 320                 ifstream inOligos;
 321                 openInputFile(oligoFile, inOligos);
 322
 323                 ofstream test;
 324
 325                 string type, oligo, group;
 326                 int index=0;
 327
 328                 while(!inOligos.eof()){
 329                         inOligos >> type;
 330
 331                         if(type[0] == '#'){
 332                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 333                         }
 334                         else{
 335                                 inOligos >> oligo;
 336
 337                                 for(int i=0;i<oligo.length();i++){
 338                                         oligo[i] = toupper(oligo[i]);
 339                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 340                                 }
 341
 342                                 if(type == "forward"){
 343                                         forPrimer.push_back(oligo);
 344                                 }
 345                                 else if(type == "reverse"){
 346                                         Sequence oligoRC("reverse", oligo);
 347                                         oligoRC.reverseComplement();
 348                                         revPrimer.push_back(oligoRC.getUnaligned());
 349                                 }
 350                                 else if(type == "barcode"){
 351                                         inOligos >> group;
 352                                         barcodes[oligo]=index++;
 353                                         groupVector.push_back(group);
 354
 355                                         if(allFiles){
 356                                                 outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
 357                                         }
 358                                 }
 359                         }
 360                 }
 361
 362                 inOligos.close();
 363
 364                 numFPrimers = forPrimer.size();
 365                 numRPrimers = revPrimer.size();
 366
 367         }
 368         catch(exception& e) {
 369                 errorOut(e, "TrimSeqsCommand", "getOligos");
 370                 exit(1);
 371         }
 372
 373 }
 374
 375 //***************************************************************************************************************
 376
 377 bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 378         try {
 379                 string rawSequence = seq.getUnaligned();
 380                 bool success = 0;       //guilty until proven innocent
 381
 382                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 383                         string oligo = it->first;
 384                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 385                                 success = 0;
 386                                 break;
 387                         }
 388
 389                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 390                                 group = it->second;
 391                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 392                                 success = 1;
 393                                 break;
 394                         }
 395                 }
 396                 return success;
 397
 398         }
 399         catch(exception& e) {
 400                 errorOut(e, "TrimSeqsCommand", "stripBarcode");
 401                 exit(1);
 402         }
 403
 404 }
 405
 406 //***************************************************************************************************************
 407
 408 bool TrimSeqsCommand::stripForward(Sequence& seq){
 409         try {
 410                 string rawSequence = seq.getUnaligned();
 411                 bool success = 0;       //guilty until proven innocent
 412
 413                 for(int i=0;i<numFPrimers;i++){
 414                         string oligo = forPrimer[i];
 415
 416                         if(rawSequence.length() < oligo.length()){
 417                                 success = 0;
 418                                 break;
 419                         }
 420
 421                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 422                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 423                                 success = 1;
 424                                 break;
 425                         }
 426                 }
 427
 428                 return success;
 429
 430         }
 431         catch(exception& e) {
 432                 errorOut(e, "TrimSeqsCommand", "stripForward");
 433                 exit(1);
 434         }
 435 }
 436
 437 //***************************************************************************************************************
 438
 439 bool TrimSeqsCommand::stripReverse(Sequence& seq){
 440         try {
 441                 string rawSequence = seq.getUnaligned();
 442                 bool success = 0;       //guilty until proven innocent
 443
 444                 for(int i=0;i<numRPrimers;i++){
 445                         string oligo = revPrimer[i];
 446
 447                         if(rawSequence.length() < oligo.length()){
 448                                 success = 0;
 449                                 break;
 450                         }
 451
 452                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 453                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 454                                 success = 1;
 455                                 break;
 456                         }
 457                 }
 458                 return success;
 459
 460         }
 461         catch(exception& e) {
 462                 errorOut(e, "TrimSeqsCommand", "stripReverse");
 463                 exit(1);
 464         }
 465 }
 466
 467 //***************************************************************************************************************
 468
 469 bool TrimSeqsCommand::cullLength(Sequence& seq){
 470         try {
 471
 472                 int length = seq.getNumBases();
 473                 bool success = 0;       //guilty until proven innocent
 474
 475                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
 476                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
 477                 else                                                                                            {       success = 0;    }
 478
 479                 return success;
 480
 481         }
 482         catch(exception& e) {
 483                 errorOut(e, "TrimSeqsCommand", "cullLength");
 484                 exit(1);
 485         }
 486
 487 }
 488
 489 //***************************************************************************************************************
 490
 491 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
 492         try {
 493                 int longHomoP = seq.getLongHomoPolymer();
 494                 bool success = 0;       //guilty until proven innocent
 495
 496                 if(longHomoP <= maxHomoP){      success = 1;    }
 497                 else                                    {       success = 0;    }
 498
 499                 return success;
 500         }
 501         catch(exception& e) {
 502                 errorOut(e, "TrimSeqsCommand", "cullHomoP");
 503                 exit(1);
 504         }
 505
 506 }
 507
 508 //***************************************************************************************************************
 509
 510 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
 511         try {
 512                 int numNs = seq.getAmbigBases();
 513                 bool success = 0;       //guilty until proven innocent
 514
 515                 if(numNs <= maxAmbig)   {       success = 1;    }
 516                 else                                    {       success = 0;    }
 517
 518                 return success;
 519         }
 520         catch(exception& e) {
 521                 errorOut(e, "TrimSeqsCommand", "cullAmbigs");
 522                 exit(1);
 523         }
 524
 525 }
 526
 527 //***************************************************************************************************************
 528
 529 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 530         try {
 531                 bool success = 1;
 532                 int length = oligo.length();
 533
 534                 for(int i=0;i<length;i++){
 535
 536                         if(oligo[i] != seq[i]){
 537                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 538                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 539                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 540                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 541                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 542                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 543                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 544                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 545                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 546                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 547                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 548                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 549
 550                                 if(success == 0)        {       break;  }
 551                         }
 552                         else{
 553                                 success = 1;
 554                         }
 555                 }
 556
 557                 return success;
 558         }
 559         catch(exception& e) {
 560                 errorOut(e, "TrimSeqsCommand", "compareDNASeq");
 561                 exit(1);
 562         }
 563
 564 }
 565
 566 //***************************************************************************************************************
 567
 568 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
 569         try {
 570                 string rawSequence = seq.getUnaligned();
 571                 int seqLength = rawSequence.length();
 572                 string name;
 573
 574                 qFile >> name;
 575                 if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine();       }  }
 576                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
 577
 578                 int score;
 579                 int end = seqLength;
 580
 581                 for(int i=0;i<seqLength;i++){
 582                         qFile >> score;
 583
 584                         if(score <= qThreshold){
 585                                 end = i;
 586                                 break;
 587                         }
 588                 }
 589                 for(int i=end+1;i<seqLength;i++){
 590                         qFile >> score;
 591                 }
 592
 593                 seq.setUnaligned(rawSequence.substr(0,end));
 594
 595                 return 1;
 596         }
 597         catch(exception& e) {
 598                 errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
 599                 exit(1);
 600         }
 601 }
 602
 603 //***************************************************************************************************************
 604
 605 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
 606         try {
 607                 string rawSequence = seq.getUnaligned();
 608                 int seqLength = seq.getNumBases();
 609                 bool success = 0;       //guilty until proven innocent
 610                 string name;
 611
 612                 qFile >> name;
 613                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); mothurOutEndLine();       } }
 614
 615                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
 616
 617                 float score;
 618                 float average = 0;
 619
 620                 for(int i=0;i<seqLength;i++){
 621                         qFile >> score;
 622                         average += score;
 623                 }
 624                 average /= seqLength;
 625
 626                 if(average >= qAverage) {       success = 1;    }
 627                 else                                    {       success = 0;    }
 628
 629                 return success;
 630         }
 631         catch(exception& e) {
 632                 errorOut(e, "TrimSeqsCommand", "cullQualAverage");
 633                 exit(1);
 634         }
 635 }
 636
 637 //***************************************************************************************************************