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 #include "needlemanoverlap.hpp"
  12
  13 //***************************************************************************************************************
  14
  15 TrimSeqsCommand::TrimSeqsCommand(string option)  {
  16         try {
  17
  18                 abort = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
  26                                                                         "qthreshold", "qaverage", "allfiles", "qtrim","diffs", "processors", "outputdir","inputdir"};
  27
  28                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  29
  30                         OptionParser parser(option);
  31                         map<string,string> parameters = parser.getParameters();
  32
  33                         ValidParameters validParameter;
  34                         map<string,string>::iterator it;
  35
  36                         //check to make sure all parameters are valid for command
  37                         for (it = parameters.begin(); it != parameters.end(); it++) {
  38                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  39                         }
  40
  41                         //if the user changes the input directory command factory will send this info to us in the output parameter
  42                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  43                         if (inputDir == "not found"){   inputDir = "";          }
  44                         else {
  45                                 string path;
  46                                 it = parameters.find("fasta");
  47                                 //user has given a template file
  48                                 if(it != parameters.end()){
  49                                         path = hasPath(it->second);
  50                                         //if the user has not given a path then, add inputdir. else leave path alone.
  51                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  52                                 }
  53
  54                                 it = parameters.find("oligos");
  55                                 //user has given a template file
  56                                 if(it != parameters.end()){
  57                                         path = hasPath(it->second);
  58                                         //if the user has not given a path then, add inputdir. else leave path alone.
  59                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
  60                                 }
  61
  62                                 it = parameters.find("qfile");
  63                                 //user has given a template file
  64                                 if(it != parameters.end()){
  65                                         path = hasPath(it->second);
  66                                         //if the user has not given a path then, add inputdir. else leave path alone.
  67                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
  68                                 }
  69                         }
  70
  71
  72                         //check for required parameters
  73                         fastaFile = validParameter.validFile(parameters, "fasta", true);
  74                         if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
  75                         else if (fastaFile == "not open") { abort = true; }
  76
  77                         //if the user changes the output directory command factory will send this info to us in the output parameter
  78                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  79                                 outputDir = "";
  80                                 outputDir += hasPath(fastaFile); //if user entered a file with a path then preserve it
  81                         }
  82
  83                         //check for optional parameter and set defaults
  84                         // ...at some point should added some additional type checking...
  85                         string temp;
  86                         temp = validParameter.validFile(parameters, "flip", false);
  87                         if (temp == "not found"){       flip = 0;       }
  88                         else if(isTrue(temp))   {       flip = 1;       }
  89
  90                         temp = validParameter.validFile(parameters, "oligos", true);
  91                         if (temp == "not found"){       oligoFile = "";         }
  92                         else if(temp == "not open"){    abort = true;   }
  93                         else                                    {       oligoFile = temp;               }
  94
  95                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
  96                         convert(temp, maxAmbig);
  97
  98                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
  99                         convert(temp, maxHomoP);
 100
 101                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
 102                         convert(temp, minLength);
 103
 104                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
 105                         convert(temp, maxLength);
 106
 107                         temp = validParameter.validFile(parameters, "diffs", false);            if (temp == "not found") { temp = "0"; }
 108                         convert(temp, diffs);
 109
 110                         temp = validParameter.validFile(parameters, "qfile", true);
 111                         if (temp == "not found")        {       qFileName = "";         }
 112                         else if(temp == "not open")     {       abort = true;           }
 113                         else                                            {       qFileName = temp;       }
 114
 115                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 116                         convert(temp, qThreshold);
 117
 118                         temp = validParameter.validFile(parameters, "qtrim", false);    if (temp == "not found") { temp = "F"; }
 119                         qtrim = isTrue(temp);
 120
 121                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 122                         convert(temp, qAverage);
 123
 124                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 125                         allFiles = isTrue(temp);
 126
 127                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 128                         convert(temp, processors);
 129
 130                         if(allFiles && oligoFile == ""){
 131                                 m->mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); m->mothurOutEndLine();
 132                         }
 133                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 134                                 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 135                                 qAverage=0;
 136                                 qThreshold=0;
 137                         }
 138                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 139                                 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 140                                 abort = true;
 141                         }
 142                 }
 143
 144         }
 145         catch(exception& e) {
 146                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 147                 exit(1);
 148         }
 149 }
 150 //**********************************************************************************************************************
 151
 152 void TrimSeqsCommand::help(){
 153         try {
 154                 m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 155                 m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 156                 m->mothurOut("The fasta parameter is required.\n");
 157                 m->mothurOut("The flip parameter .... The default is 0.\n");
 158                 m->mothurOut("The oligos parameter .... The default is "".\n");
 159                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 160                 m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 161                 m->mothurOut("The minlength parameter .... The default is 0.\n");
 162                 m->mothurOut("The maxlength parameter .... The default is 0.\n");
 163                 m->mothurOut("The diffs parameter .... The default is 0.\n");
 164                 m->mothurOut("The qfile parameter .....\n");
 165                 m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 166                 m->mothurOut("The qaverage parameter .... The default is 0.\n");
 167                 m->mothurOut("The allfiles parameter .... The default is F.\n");
 168                 m->mothurOut("The qtrim parameter .... The default is F.\n");
 169                 m->mothurOut("The trim.seqs command should be in the following format: \n");
 170                 m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
 171                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 172                 m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 173                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
 174                 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 175
 176         }
 177         catch(exception& e) {
 178                 m->errorOut(e, "TrimSeqsCommand", "help");
 179                 exit(1);
 180         }
 181 }
 182
 183
 184 //***************************************************************************************************************
 185
 186 TrimSeqsCommand::~TrimSeqsCommand(){    /*      do nothing      */      }
 187
 188 //***************************************************************************************************************
 189
 190 int TrimSeqsCommand::execute(){
 191         try{
 192
 193                 if (abort == true) { return 0; }
 194
 195                 numFPrimers = 0;  //this needs to be initialized
 196                 numRPrimers = 0;
 197
 198                 string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
 199                 outputNames.push_back(trimSeqFile);
 200                 string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
 201                 outputNames.push_back(scrapSeqFile);
 202                 string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
 203
 204                 vector<string> fastaFileNames;
 205                 if(oligoFile != ""){
 206                         outputNames.push_back(groupFile);
 207                         getOligos(fastaFileNames);
 208                 }
 209
 210                 if(qFileName != "")     {       setLines(qFileName, qLines);    }
 211
 212
 213                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 214                                 if(processors == 1){
 215                                         ifstream inFASTA;
 216                                         openInputFile(fastaFile, inFASTA);
 217                                         int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 218                                         inFASTA.close();
 219
 220                                         lines.push_back(new linePair(0, numSeqs));
 221
 222                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 223
 224                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 225                                                 rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
 226                                         }
 227
 228                                 }else{
 229                                         setLines(fastaFile, lines);
 230                                         if(qFileName == "")     {       qLines = lines; }
 231
 232                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames);
 233
 234                                         rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
 235                                         rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
 236                                         rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
 237                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 238                                                 rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
 239                                         }
 240                                         //append files
 241                                         for(int i=1;i<processors;i++){
 242                                                 appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
 243                                                 remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
 244                                                 appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
 245                                                 remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
 246                                                 appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 247                                                 remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 248                                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 249                                                         appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
 250                                                         remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 251                                                 }
 252                                         }
 253                                 }
 254
 255                                 if (m->control_pressed) {  return 0; }
 256                 #else
 257                                 ifstream inFASTA;
 258                                 openInputFile(fastafileNames[s], inFASTA);
 259                                 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 260                                 inFASTA.close();
 261
 262                                 lines.push_back(new linePair(0, numSeqs));
 263
 264                                 driverCreateSummary(fastafile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 265
 266                                 if (m->control_pressed) {  return 0; }
 267                 #endif
 268
 269
 270                 for(int i=0;i<fastaFileNames.size();i++){
 271                         ifstream inFASTA;
 272                         string seqName;
 273                         openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
 274                         ofstream outGroups;
 275                         openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
 276                         outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
 277
 278                         while(!inFASTA.eof()){
 279                                 if(inFASTA.get() == '>'){
 280                                         inFASTA >> seqName;
 281                                         outGroups << seqName << '\t' << groupVector[i] << endl;
 282                                 }
 283                                 while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 284                         }
 285                         outGroups.close();
 286                         inFASTA.close();
 287                 }
 288
 289                 if (m->control_pressed) {
 290                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 291                         return 0;
 292                 }
 293
 294                 m->mothurOutEndLine();
 295                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 296                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 297                 m->mothurOutEndLine();
 298
 299                 return 0;
 300
 301         }
 302         catch(exception& e) {
 303                 m->errorOut(e, "TrimSeqsCommand", "execute");
 304                 exit(1);
 305         }
 306 }
 307
 308 /**************************************************************************************/
 309 int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames, linePair* line, linePair* qline) {
 310         try {
 311
 312                 ofstream outFASTA;
 313                 int able = openOutputFile(trimFile, outFASTA);
 314
 315                 ofstream scrapFASTA;
 316                 openOutputFile(scrapFile, scrapFASTA);
 317
 318                 ofstream outGroups;
 319                 vector<ofstream*> fastaFileNames;
 320                 if (oligoFile != "") {
 321                         openOutputFile(groupFile, outGroups);
 322                         for (int i = 0; i < fastaNames.size(); i++) {
 323                                 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 324                         }
 325                 }
 326
 327                 ifstream inFASTA;
 328                 openInputFile(filename, inFASTA);
 329
 330                 ifstream qFile;
 331                 if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
 332
 333                 qFile.seekg(qline->start);
 334                 inFASTA.seekg(line->start);
 335
 336                 for(int i=0;i<line->num;i++){
 337
 338                         if (m->control_pressed) {
 339                                 inFASTA.close();
 340                                 outFASTA.close();
 341                                 scrapFASTA.close();
 342                                 if (oligoFile != "") {   outGroups.close();   }
 343                                 if(qFileName != "")     {       qFile.close();  }
 344                                 for(int i=0;i<fastaFileNames.size();i++){
 345                                         fastaFileNames[i]->close();
 346                                         delete fastaFileNames[i];
 347                                 }
 348                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 349                                 return 0;
 350                         }
 351
 352                         bool success = 1;
 353
 354                         Sequence currSeq(inFASTA);
 355
 356                         string origSeq = currSeq.getUnaligned();
 357                         if (origSeq != "") {
 358                                 int group;
 359                                 string trashCode = "";
 360
 361                                 if(qFileName != ""){
 362                                         if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
 363                                         else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
 364                                         if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) {
 365                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 366                                         }
 367                                         if(!success)                    {       trashCode += 'q';                                                               }
 368                                 }
 369
 370                                 if(barcodes.size() != 0){
 371                                         success = stripBarcode(currSeq, group);
 372                                         if(!success){   trashCode += 'b';       }
 373                                 }
 374
 375                                 if(numFPrimers != 0){
 376                                         success = stripForward(currSeq);
 377                                         if(!success){   trashCode += 'f';       }
 378                                 }
 379
 380                                 if(numRPrimers != 0){
 381                                         success = stripReverse(currSeq);
 382                                         if(!success){   trashCode += 'r';       }
 383                                 }
 384
 385                                 if(minLength > 0 || maxLength > 0){
 386                                         success = cullLength(currSeq);
 387                                         if(!success){   trashCode += 'l'; }
 388                                 }
 389                                 if(maxHomoP > 0){
 390                                         success = cullHomoP(currSeq);
 391                                         if(!success){   trashCode += 'h';       }
 392                                 }
 393                                 if(maxAmbig != -1){
 394                                         success = cullAmbigs(currSeq);
 395                                         if(!success){   trashCode += 'n';       }
 396                                 }
 397
 398                                 if(flip){       currSeq.reverseComplement();    }               // should go last
 399
 400                                 if(trashCode.length() == 0){
 401                                         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.
 402                                         currSeq.printSequence(outFASTA);
 403                                         if(barcodes.size() != 0){
 404                                                 outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
 405
 406                                                 if(allFiles){
 407                                                         currSeq.printSequence(*fastaFileNames[group]);
 408                                                 }
 409                                         }
 410                                 }
 411                                 else{
 412                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 413                                         currSeq.setUnaligned(origSeq);
 414                                         currSeq.printSequence(scrapFASTA);
 415                                 }
 416                         }
 417                         gobble(inFASTA);
 418                 }
 419
 420                 inFASTA.close();
 421                 outFASTA.close();
 422                 scrapFASTA.close();
 423                 if (oligoFile != "") {   outGroups.close();   }
 424                 if(qFileName != "")     {       qFile.close();  }
 425
 426                 for(int i=0;i<fastaFileNames.size();i++){
 427                         fastaFileNames[i]->close();
 428                         delete fastaFileNames[i];
 429                 }
 430
 431                 return 0;
 432         }
 433         catch(exception& e) {
 434                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 435                 exit(1);
 436         }
 437 }
 438 /**************************************************************************************************/
 439 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames) {
 440         try {
 441 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 442                 int process = 0;
 443                 int exitCommand = 1;
 444                 processIDS.clear();
 445
 446                 //loop through and create all the processes you want
 447                 while (process != processors) {
 448                         int pid = fork();
 449
 450                         if (pid > 0) {
 451                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 452                                 process++;
 453                         }else if (pid == 0){
 454                                 driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, lines[process], qLines[process]);
 455                                 exit(0);
 456                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 457                 }
 458
 459                 //force parent to wait until all the processes are done
 460                 for (int i=0;i<processors;i++) {
 461                         int temp = processIDS[i];
 462                         wait(&temp);
 463                 }
 464
 465                 return exitCommand;
 466 #endif
 467         }
 468         catch(exception& e) {
 469                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 470                 exit(1);
 471         }
 472 }
 473 /**************************************************************************************************/
 474
 475 int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
 476         try {
 477
 478                 lines.clear();
 479
 480                 vector<long int> positions;
 481
 482                 ifstream inFASTA;
 483                 openInputFile(filename, inFASTA);
 484
 485                 string input;
 486                 while(!inFASTA.eof()){
 487                         input = getline(inFASTA);
 488
 489                         if (input.length() != 0) {
 490                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 491                         }
 492                 }
 493                 inFASTA.close();
 494
 495                 int numFastaSeqs = positions.size();
 496
 497                 FILE * pFile;
 498                 long size;
 499
 500                 //get num bytes in file
 501                 pFile = fopen (filename.c_str(),"rb");
 502                 if (pFile==NULL) perror ("Error opening file");
 503                 else{
 504                         fseek (pFile, 0, SEEK_END);
 505                         size=ftell (pFile);
 506                         fclose (pFile);
 507                 }
 508
 509                 int numSeqsPerProcessor = numFastaSeqs / processors;
 510
 511                 for (int i = 0; i < processors; i++) {
 512
 513                         long int startPos = positions[ i * numSeqsPerProcessor ];
 514                         if(i == processors - 1){
 515                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 516                         }else{
 517                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 518                         }
 519                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 520                 }
 521
 522                 return numFastaSeqs;
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 526                 exit(1);
 527         }
 528 }
 529 //***************************************************************************************************************
 530
 531 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*>& outFASTAVec
 532         try {
 533                 ifstream inOligos;
 534                 openInputFile(oligoFile, inOligos);
 535
 536                 ofstream test;
 537
 538                 string type, oligo, group;
 539                 int index=0;
 540
 541                 while(!inOligos.eof()){
 542                         inOligos >> type;
 543
 544                         if(type[0] == '#'){
 545                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 546                         }
 547                         else{
 548                                 inOligos >> oligo;
 549
 550                                 for(int i=0;i<oligo.length();i++){
 551                                         oligo[i] = toupper(oligo[i]);
 552                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 553                                 }
 554
 555                                 if(type == "forward"){
 556                                         forPrimer.push_back(oligo);
 557                                 }
 558                                 else if(type == "reverse"){
 559                                         Sequence oligoRC("reverse", oligo);
 560                                         oligoRC.reverseComplement();
 561                                         revPrimer.push_back(oligoRC.getUnaligned());
 562                                 }
 563                                 else if(type == "barcode"){
 564                                         inOligos >> group;
 565                                         barcodes[oligo]=index++;
 566                                         groupVector.push_back(group);
 567
 568                                         if(allFiles){
 569                                                 //outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
 570                                                 outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 571                                                 outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 572                                         }
 573                                 }
 574                         }
 575                 }
 576
 577                 inOligos.close();
 578
 579                 numFPrimers = forPrimer.size();
 580                 numRPrimers = revPrimer.size();
 581
 582         }
 583         catch(exception& e) {
 584                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 585                 exit(1);
 586         }
 587 }
 588 //***************************************************************************************************************
 589
 590 bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 591         try {
 592                 string rawSequence = seq.getUnaligned();
 593                 bool success = 0;       //guilty until proven innocent
 594
 595                 //can you find the barcode
 596                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 597                         string oligo = it->first;
 598                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 599                                 success = 0;
 600                                 break;
 601                         }
 602
 603                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 604                                 group = it->second;
 605                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 606                                 success = 1;
 607                                 break;
 608                         }
 609                 }
 610
 611                 //if you found the barcode or if you don't want to allow for diffs
 612                 if ((diffs == 0) || (success == 1)) { return success;  }
 613
 614                 else { //try aligning and see if you can find it
 615
 616                         Alignment* alignment;
 617                         if (barcodes.size() > 0) { //assumes barcodes are all the same length
 618                                 map<string,int>::iterator it=barcodes.begin();
 619                                 string temp = it->first;
 620
 621                                 alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (temp.length()+diffs+1));
 622                         }else{ alignment = NULL; }
 623
 624
 625                         //can you find the barcode
 626                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 627                                 string oligo = it->first;
 628                                 int length = oligo.length();
 629
 630                                 if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 631                                         success = 0;
 632                                         break;
 633                                 }
 634
 635                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 636                                 alignment->align(oligo, rawSequence.substr(0,length+diffs));
 637                                 oligo = alignment->getSeqAAln();
 638                                 string temp = alignment->getSeqBAln();
 639                 cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,oligo.length()) << " raw aligned = " << temp << endl;
 640
 641                                 int newStart=0;
 642                                 if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
 643                 cout << "found match" << endl;
 644                                         group = it->second;
 645                                         seq.setUnaligned(rawSequence.substr(newStart));
 646                                         success = 1;
 647                                         break;
 648                                 }
 649                         }
 650
 651                         if (alignment != NULL) {  delete alignment;  }
 652                 }
 653                 return success;
 654
 655         }
 656         catch(exception& e) {
 657                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
 658                 exit(1);
 659         }
 660
 661 }
 662
 663 //***************************************************************************************************************
 664
 665 bool TrimSeqsCommand::stripForward(Sequence& seq){
 666         try {
 667                 string rawSequence = seq.getUnaligned();
 668                 bool success = 0;       //guilty until proven innocent
 669
 670                 for(int i=0;i<numFPrimers;i++){
 671                         string oligo = forPrimer[i];
 672
 673                         if(rawSequence.length() < oligo.length()){
 674                                 success = 0;
 675                                 break;
 676                         }
 677
 678                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 679                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 680                                 success = 1;
 681                                 break;
 682                         }
 683                 }
 684
 685                 //if you found the primer or if you don't want to allow for diffs
 686                 if ((diffs == 0) || (success == 1)) { return success;  }
 687
 688                 else { //try aligning and see if you can find it
 689
 690
 691                         Alignment* alignment;
 692                         if (numFPrimers > 0) { alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (forPrimer[0].length()+diffs+1));  } //assumes primers are all the same length
 693                         else{ alignment = NULL; }
 694
 695                         //can you find the primer
 696                         for(int i=0;i<numFPrimers;i++){
 697                                 string oligo = forPrimer[i];
 698                                 int length = oligo.length();
 699
 700                                 if(rawSequence.length() < oligo.length()){
 701                                         success = 0;
 702                                         break;
 703                                 }
 704
 705                                 //use needleman to align first primer.length()+numdiffs of sequence to each primer
 706                                 alignment->align(oligo, rawSequence.substr(0,length+diffs));
 707                                 oligo = alignment->getSeqAAln();
 708
 709                                 int newStart = 0;
 710                                 if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
 711                                         seq.setUnaligned(rawSequence.substr(newStart));
 712                                         success = 1;
 713                                         break;
 714                                 }
 715                         }
 716
 717                         if (alignment != NULL) {  delete alignment;  }
 718                 }
 719
 720                 return success;
 721
 722         }
 723         catch(exception& e) {
 724                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
 725                 exit(1);
 726         }
 727 }
 728
 729 //***************************************************************************************************************
 730
 731 bool TrimSeqsCommand::stripReverse(Sequence& seq){
 732         try {
 733                 string rawSequence = seq.getUnaligned();
 734                 bool success = 0;       //guilty until proven innocent
 735
 736                 for(int i=0;i<numRPrimers;i++){
 737                         string oligo = revPrimer[i];
 738
 739                         if(rawSequence.length() < oligo.length()){
 740                                 success = 0;
 741                                 break;
 742                         }
 743
 744                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 745                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 746                                 success = 1;
 747                                 break;
 748                         }
 749                 }
 750                 return success;
 751
 752         }
 753         catch(exception& e) {
 754                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
 755                 exit(1);
 756         }
 757 }
 758
 759 //***************************************************************************************************************
 760
 761 bool TrimSeqsCommand::cullLength(Sequence& seq){
 762         try {
 763
 764                 int length = seq.getNumBases();
 765                 bool success = 0;       //guilty until proven innocent
 766
 767                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
 768                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
 769                 else                                                                                            {       success = 0;    }
 770
 771                 return success;
 772
 773         }
 774         catch(exception& e) {
 775                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
 776                 exit(1);
 777         }
 778
 779 }
 780
 781 //***************************************************************************************************************
 782
 783 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
 784         try {
 785                 int longHomoP = seq.getLongHomoPolymer();
 786                 bool success = 0;       //guilty until proven innocent
 787
 788                 if(longHomoP <= maxHomoP){      success = 1;    }
 789                 else                                    {       success = 0;    }
 790
 791                 return success;
 792         }
 793         catch(exception& e) {
 794                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
 795                 exit(1);
 796         }
 797
 798 }
 799
 800 //***************************************************************************************************************
 801
 802 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
 803         try {
 804                 int numNs = seq.getAmbigBases();
 805                 bool success = 0;       //guilty until proven innocent
 806
 807                 if(numNs <= maxAmbig)   {       success = 1;    }
 808                 else                                    {       success = 0;    }
 809
 810                 return success;
 811         }
 812         catch(exception& e) {
 813                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
 814                 exit(1);
 815         }
 816
 817 }
 818
 819 //***************************************************************************************************************
 820
 821 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 822         try {
 823                 bool success = 1;
 824                 int length = oligo.length();
 825
 826                 for(int i=0;i<length;i++){
 827
 828                         if(oligo[i] != seq[i]){
 829                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 830                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 831                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 832                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 833                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 834                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 835                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 836                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 837                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 838                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 839                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 840                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 841
 842                                 if(success == 0)        {       break;   }
 843                         }
 844                         else{
 845                                 success = 1;
 846                         }
 847                 }
 848
 849                 return success;
 850         }
 851         catch(exception& e) {
 852                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
 853                 exit(1);
 854         }
 855
 856 }
 857 //***************************************************************************************************************
 858
 859 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq, int numBases, int& end){
 860         try {
 861                 bool success = 1;
 862                 int length = oligo.length();
 863                 end = length;
 864                 int countBases = 0;
 865                 int countDiffs = 0;
 866
 867                 if (length != 0) {
 868                         if ((oligo[0] == '-') || (oligo[0] == '.')) {  success = 0; return success;  } //no gaps allowed at beginning
 869                 }
 870
 871                 for(int i=0;i<length;i++){
 872
 873                         if ((oligo[i] != '-') && (oligo[i] != '.'))  { countBases++; }
 874
 875         //cout << oligo[i] << " " << seq[i] << " diffs = " << countDiffs << " countBases = " << countBases << endl;
 876
 877                         if(oligo[i] != seq[i]){
 878                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
 879                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
 880                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
 881                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
 882                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
 883                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
 884                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
 885                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
 886                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 887                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 888                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
 889                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
 890
 891                                 if(countDiffs > diffs)  {       success = 0; break;      }
 892                         }
 893                         else{
 894                                 success = 1;
 895                         }
 896
 897                         if (countBases >= numBases) { end = i; break; } //stop checking after end of barcode or primer
 898                 }
 899
 900                 return success;
 901         }
 902         catch(exception& e) {
 903                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
 904                 exit(1);
 905         }
 906
 907 }
 908 //***************************************************************************************************************
 909
 910 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
 911         try {
 912                 string rawSequence = seq.getUnaligned();
 913                 int seqLength;  // = rawSequence.length();
 914                 string name, temp, temp2;
 915
 916                 qFile >> name >> temp;
 917
 918                 splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
 919                 convert(temp, seqLength); //converts string to int
 920
 921                 if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); }  }
 922                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
 923
 924                 int score;
 925                 int end = seqLength;
 926
 927                 for(int i=0;i<seqLength;i++){
 928                         qFile >> score;
 929
 930                         if(score <= qThreshold){
 931                                 end = i;
 932                                 break;
 933                         }
 934                 }
 935                 for(int i=end+1;i<seqLength;i++){
 936                         qFile >> score;
 937                 }
 938
 939                 seq.setUnaligned(rawSequence.substr(0,end));
 940
 941                 return 1;
 942         }
 943         catch(exception& e) {
 944                 m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
 945                 exit(1);
 946         }
 947 }
 948
 949 //***************************************************************************************************************
 950
 951 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
 952         try {
 953                 string rawSequence = seq.getUnaligned();
 954                 int seqLength = seq.getNumBases();
 955                 bool success = 0;       //guilty until proven innocent
 956                 string name;
 957
 958                 qFile >> name;
 959                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
 960
 961                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
 962
 963                 float score;
 964                 float average = 0;
 965
 966                 for(int i=0;i<seqLength;i++){
 967                         qFile >> score;
 968                         average += score;
 969                 }
 970                 average /= seqLength;
 971
 972                 if(average >= qAverage) {       success = 1;    }
 973                 else                                    {       success = 0;    }
 974
 975                 return success;
 976         }
 977         catch(exception& e) {
 978                 m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
 979                 exit(1);
 980         }
 981 }
 982
 983 //***************************************************************************************************************