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","tdiffs", "pdiffs", "bdiffs", "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
 108                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found") { temp = "0"; }
 109                         convert(temp, bdiffs);
 110
 111                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 112                         convert(temp, pdiffs);
 113
 114                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 115                         convert(temp, tdiffs);
 116
 117                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 118
 119                         temp = validParameter.validFile(parameters, "qfile", true);
 120                         if (temp == "not found")        {       qFileName = "";         }
 121                         else if(temp == "not open")     {       abort = true;           }
 122                         else                                            {       qFileName = temp;       }
 123
 124                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 125                         convert(temp, qThreshold);
 126
 127                         temp = validParameter.validFile(parameters, "qtrim", false);    if (temp == "not found") { temp = "F"; }
 128                         qtrim = isTrue(temp);
 129
 130                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 131                         convert(temp, qAverage);
 132
 133                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 134                         allFiles = isTrue(temp);
 135
 136                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 137                         convert(temp, processors);
 138
 139                         if(allFiles && oligoFile == ""){
 140                                 m->mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); m->mothurOutEndLine();
 141                         }
 142                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 143                                 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 144                                 qAverage=0;
 145                                 qThreshold=0;
 146                         }
 147                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 148                                 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 149                                 abort = true;
 150                         }
 151                 }
 152
 153         }
 154         catch(exception& e) {
 155                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 156                 exit(1);
 157         }
 158 }
 159 //**********************************************************************************************************************
 160
 161 void TrimSeqsCommand::help(){
 162         try {
 163                 m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 164                 m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 165                 m->mothurOut("The fasta parameter is required.\n");
 166                 m->mothurOut("The flip parameter .... The default is 0.\n");
 167                 m->mothurOut("The oligos parameter .... The default is "".\n");
 168                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 169                 m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 170                 m->mothurOut("The minlength parameter .... The default is 0.\n");
 171                 m->mothurOut("The maxlength parameter .... The default is 0.\n");
 172                 m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
 173                 m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
 174                 m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
 175                 m->mothurOut("The qfile parameter .....\n");
 176                 m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 177                 m->mothurOut("The qaverage parameter .... The default is 0.\n");
 178                 m->mothurOut("The allfiles parameter .... The default is F.\n");
 179                 m->mothurOut("The qtrim parameter .... The default is F.\n");
 180                 m->mothurOut("The trim.seqs command should be in the following format: \n");
 181                 m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
 182                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 183                 m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 184                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
 185                 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 186
 187         }
 188         catch(exception& e) {
 189                 m->errorOut(e, "TrimSeqsCommand", "help");
 190                 exit(1);
 191         }
 192 }
 193
 194
 195 //***************************************************************************************************************
 196
 197 TrimSeqsCommand::~TrimSeqsCommand(){    /*      do nothing      */      }
 198
 199 //***************************************************************************************************************
 200
 201 int TrimSeqsCommand::execute(){
 202         try{
 203
 204                 if (abort == true) { return 0; }
 205
 206                 numFPrimers = 0;  //this needs to be initialized
 207                 numRPrimers = 0;
 208
 209                 string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
 210                 outputNames.push_back(trimSeqFile);
 211                 string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
 212                 outputNames.push_back(scrapSeqFile);
 213                 string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
 214
 215                 vector<string> fastaFileNames;
 216                 if(oligoFile != ""){
 217                         outputNames.push_back(groupFile);
 218                         getOligos(fastaFileNames);
 219                 }
 220
 221                 if(qFileName != "")     {       setLines(qFileName, qLines);    }
 222
 223
 224                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 225                                 if(processors == 1){
 226                                         ifstream inFASTA;
 227                                         openInputFile(fastaFile, inFASTA);
 228                                         int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 229                                         inFASTA.close();
 230
 231                                         lines.push_back(new linePair(0, numSeqs));
 232
 233                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 234
 235                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 236                                                 rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
 237                                         }
 238
 239                                 }else{
 240                                         setLines(fastaFile, lines);
 241                                         if(qFileName == "")     {       qLines = lines; }
 242
 243                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames);
 244
 245                                         rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
 246                                         rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
 247                                         rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
 248                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 249                                                 rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
 250                                         }
 251                                         //append files
 252                                         for(int i=1;i<processors;i++){
 253                                                 appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
 254                                                 remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
 255                                                 appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
 256                                                 remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
 257                                                 appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 258                                                 remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 259                                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 260                                                         appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
 261                                                         remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 262                                                 }
 263                                         }
 264                                 }
 265
 266                                 if (m->control_pressed) {  return 0; }
 267                 #else
 268                                 ifstream inFASTA;
 269                                 openInputFile(fastafileNames[s], inFASTA);
 270                                 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 271                                 inFASTA.close();
 272
 273                                 lines.push_back(new linePair(0, numSeqs));
 274
 275                                 driverCreateSummary(fastafile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 276
 277                                 if (m->control_pressed) {  return 0; }
 278                 #endif
 279
 280
 281                 for(int i=0;i<fastaFileNames.size();i++){
 282                         ifstream inFASTA;
 283                         string seqName;
 284                         openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
 285                         ofstream outGroups;
 286                         openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
 287                         outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
 288
 289                         while(!inFASTA.eof()){
 290                                 if(inFASTA.get() == '>'){
 291                                         inFASTA >> seqName;
 292                                         outGroups << seqName << '\t' << groupVector[i] << endl;
 293                                 }
 294                                 while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 295                         }
 296                         outGroups.close();
 297                         inFASTA.close();
 298                 }
 299
 300                 if (m->control_pressed) {
 301                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 302                         return 0;
 303                 }
 304
 305                 m->mothurOutEndLine();
 306                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 307                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 308                 m->mothurOutEndLine();
 309
 310                 return 0;
 311
 312         }
 313         catch(exception& e) {
 314                 m->errorOut(e, "TrimSeqsCommand", "execute");
 315                 exit(1);
 316         }
 317 }
 318
 319 /**************************************************************************************/
 320 int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames, linePair* line, linePair* qline) {
 321         try {
 322
 323                 ofstream outFASTA;
 324                 int able = openOutputFile(trimFile, outFASTA);
 325
 326                 ofstream scrapFASTA;
 327                 openOutputFile(scrapFile, scrapFASTA);
 328
 329                 ofstream outGroups;
 330                 vector<ofstream*> fastaFileNames;
 331                 if (oligoFile != "") {
 332                         openOutputFile(groupFile, outGroups);
 333                         for (int i = 0; i < fastaNames.size(); i++) {
 334                                 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 335                         }
 336                 }
 337
 338                 ifstream inFASTA;
 339                 openInputFile(filename, inFASTA);
 340
 341                 ifstream qFile;
 342                 if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
 343
 344                 qFile.seekg(qline->start);
 345                 inFASTA.seekg(line->start);
 346
 347                 for(int i=0;i<line->num;i++){
 348
 349                         if (m->control_pressed) {
 350                                 inFASTA.close();
 351                                 outFASTA.close();
 352                                 scrapFASTA.close();
 353                                 if (oligoFile != "") {   outGroups.close();   }
 354                                 if(qFileName != "")     {       qFile.close();  }
 355                                 for(int i=0;i<fastaFileNames.size();i++){
 356                                         fastaFileNames[i]->close();
 357                                         delete fastaFileNames[i];
 358                                 }
 359                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 360                                 return 0;
 361                         }
 362
 363                         bool success = 1;
 364
 365                         Sequence currSeq(inFASTA);
 366
 367                         string origSeq = currSeq.getUnaligned();
 368                         if (origSeq != "") {
 369                                 int group;
 370                                 string trashCode = "";
 371                                 int currentSeqsDiffs = 0;
 372
 373                                 if(qFileName != ""){
 374                                         if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
 375                                         else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
 376                                         if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) {
 377                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 378                                         }
 379                                         if(!success)                    {       trashCode += 'q';                                                               }
 380                                 }
 381
 382                                 if(barcodes.size() != 0){
 383                                         success = stripBarcode(currSeq, group);
 384 //                                      cout << "here: " << success << endl;
 385                                         if(success > bdiffs){   trashCode += 'b';       }
 386                                         else{ currentSeqsDiffs += success;  }
 387                                 }
 388
 389                                 if(numFPrimers != 0){
 390                                         success = stripForward(currSeq);
 391                                         if(success > pdiffs){   trashCode += 'f';       }
 392                                         else{ currentSeqsDiffs += success;  }
 393                                 }
 394
 395                                 if (currentSeqsDiffs > tdiffs) { trashCode += 't';   }
 396
 397                                 if(numRPrimers != 0){
 398                                         success = stripReverse(currSeq);
 399                                         if(!success){   trashCode += 'r';       }
 400                                 }
 401
 402                                 if(minLength > 0 || maxLength > 0){
 403                                         success = cullLength(currSeq);
 404                                         if(!success){   trashCode += 'l'; }
 405                                 }
 406                                 if(maxHomoP > 0){
 407                                         success = cullHomoP(currSeq);
 408                                         if(!success){   trashCode += 'h';       }
 409                                 }
 410                                 if(maxAmbig != -1){
 411                                         success = cullAmbigs(currSeq);
 412                                         if(!success){   trashCode += 'n';       }
 413                                 }
 414
 415                                 if(flip){       currSeq.reverseComplement();    }               // should go last
 416
 417                                 if(trashCode.length() == 0){
 418                                         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.
 419                                         currSeq.printSequence(outFASTA);
 420                                         if(barcodes.size() != 0){
 421                                                 outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
 422
 423                                                 if(allFiles){
 424                                                         currSeq.printSequence(*fastaFileNames[group]);
 425                                                 }
 426                                         }
 427                                 }
 428                                 else{
 429                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 430                                         currSeq.setUnaligned(origSeq);
 431                                         currSeq.printSequence(scrapFASTA);
 432                                 }
 433                         }
 434                         gobble(inFASTA);
 435                 }
 436
 437                 inFASTA.close();
 438                 outFASTA.close();
 439                 scrapFASTA.close();
 440                 if (oligoFile != "") {   outGroups.close();   }
 441                 if(qFileName != "")     {       qFile.close();  }
 442
 443                 for(int i=0;i<fastaFileNames.size();i++){
 444                         fastaFileNames[i]->close();
 445                         delete fastaFileNames[i];
 446                 }
 447
 448                 return 0;
 449         }
 450         catch(exception& e) {
 451                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 452                 exit(1);
 453         }
 454 }
 455 /**************************************************************************************************/
 456 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames) {
 457         try {
 458 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 459                 int process = 0;
 460                 int exitCommand = 1;
 461                 processIDS.clear();
 462
 463                 //loop through and create all the processes you want
 464                 while (process != processors) {
 465                         int pid = fork();
 466
 467                         if (pid > 0) {
 468                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 469                                 process++;
 470                         }else if (pid == 0){
 471                                 driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, lines[process], qLines[process]);
 472                                 exit(0);
 473                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 474                 }
 475
 476                 //force parent to wait until all the processes are done
 477                 for (int i=0;i<processors;i++) {
 478                         int temp = processIDS[i];
 479                         wait(&temp);
 480                 }
 481
 482                 return exitCommand;
 483 #endif
 484         }
 485         catch(exception& e) {
 486                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 487                 exit(1);
 488         }
 489 }
 490 /**************************************************************************************************/
 491
 492 int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
 493         try {
 494
 495                 lines.clear();
 496
 497                 vector<long int> positions;
 498
 499                 ifstream inFASTA;
 500                 openInputFile(filename, inFASTA);
 501
 502                 string input;
 503                 while(!inFASTA.eof()){
 504                         input = getline(inFASTA);
 505
 506                         if (input.length() != 0) {
 507                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 508                         }
 509                 }
 510                 inFASTA.close();
 511
 512                 int numFastaSeqs = positions.size();
 513
 514                 FILE * pFile;
 515                 long size;
 516
 517                 //get num bytes in file
 518                 pFile = fopen (filename.c_str(),"rb");
 519                 if (pFile==NULL) perror ("Error opening file");
 520                 else{
 521                         fseek (pFile, 0, SEEK_END);
 522                         size=ftell (pFile);
 523                         fclose (pFile);
 524                 }
 525
 526                 int numSeqsPerProcessor = numFastaSeqs / processors;
 527
 528                 for (int i = 0; i < processors; i++) {
 529
 530                         long int startPos = positions[ i * numSeqsPerProcessor ];
 531                         if(i == processors - 1){
 532                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 533                         }else{
 534                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 535                         }
 536                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 537                 }
 538
 539                 return numFastaSeqs;
 540         }
 541         catch(exception& e) {
 542                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 543                 exit(1);
 544         }
 545 }
 546 //***************************************************************************************************************
 547
 548 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*>& outFASTAVec
 549         try {
 550                 ifstream inOligos;
 551                 openInputFile(oligoFile, inOligos);
 552
 553                 ofstream test;
 554
 555                 string type, oligo, group;
 556                 int index=0;
 557
 558                 while(!inOligos.eof()){
 559                         inOligos >> type;
 560
 561                         if(type[0] == '#'){
 562                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 563                         }
 564                         else{
 565                                 inOligos >> oligo;
 566
 567                                 for(int i=0;i<oligo.length();i++){
 568                                         oligo[i] = toupper(oligo[i]);
 569                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 570                                 }
 571
 572                                 if(type == "forward"){
 573                                         forPrimer.push_back(oligo);
 574                                 }
 575                                 else if(type == "reverse"){
 576                                         Sequence oligoRC("reverse", oligo);
 577                                         oligoRC.reverseComplement();
 578                                         revPrimer.push_back(oligoRC.getUnaligned());
 579                                 }
 580                                 else if(type == "barcode"){
 581                                         inOligos >> group;
 582                                         barcodes[oligo]=index++;
 583                                         groupVector.push_back(group);
 584
 585                                         if(allFiles){
 586                                                 //outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
 587                                                 outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 588                                                 outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 589                                         }
 590                                 }
 591                         }
 592                 }
 593
 594                 inOligos.close();
 595
 596                 numFPrimers = forPrimer.size();
 597                 numRPrimers = revPrimer.size();
 598
 599         }
 600         catch(exception& e) {
 601                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 602                 exit(1);
 603         }
 604 }
 605 //***************************************************************************************************************
 606
 607 int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 608         try {
 609                 string rawSequence = seq.getUnaligned();
 610                 bool success = bdiffs + 1;      //guilty until proven innocent
 611
 612                 //can you find the barcode
 613                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 614                         string oligo = it->first;
 615                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 616                                 success = bdiffs + 1;
 617                                 break;
 618                         }
 619
 620                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 621                                 group = it->second;
 622                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 623                                 success = 0;
 624                                 break;
 625                         }
 626                 }
 627
 628                 //if you found the barcode or if you don't want to allow for diffs
 629 //              cout << success;
 630                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 631
 632                 else { //try aligning and see if you can find it
 633 //                      cout << endl;
 634
 635                         int maxLength = 0;
 636
 637                         Alignment* alignment;
 638                         if (barcodes.size() > 0) {
 639                                 map<string,int>::iterator it=barcodes.begin();
 640
 641                                 for(it;it!=barcodes.end();it++){
 642                                         if(it->first.length() > maxLength){
 643                                                 maxLength = it->first.length();
 644                                         }
 645                                 }
 646                                 alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+bdiffs+1));
 647
 648                         }else{ alignment = NULL; }
 649
 650                         //can you find the barcode
 651                         int minDiff = 1e6;
 652                         int minCount = 1;
 653                         int minGroup = -1;
 654                         int minPos = 0;
 655
 656                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 657                                 string oligo = it->first;
 658 //                              int length = oligo.length();
 659
 660                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 661                                         success = bdiffs + 1;
 662                                         break;
 663                                 }
 664
 665                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 666                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 667                                 oligo = alignment->getSeqAAln();
 668                                 string temp = alignment->getSeqBAln();
 669
 670                                 int alnLength = oligo.length();
 671
 672                                 for(int i=oligo.length()-1;i>=0;i--){
 673                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 674                                 }
 675                                 oligo = oligo.substr(0,alnLength);
 676                                 temp = temp.substr(0,alnLength);
 677 //                              cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,alnLength) << " raw aligned = " << temp << endl;
 678                                 cout << seq.getName() << endl;
 679                                 cout << temp << endl;
 680                                 cout << oligo << endl;
 681                                 cout << alnLength << endl;
 682                                 cout << endl;
 683
 684                                 int newStart=0;
 685                                 int numDiff = countDiffs(oligo, temp);
 686                                 if(numDiff < minDiff){
 687                                         minDiff = numDiff;
 688                                         minCount = 1;
 689                                         minGroup = it->second;
 690                                         minPos = 0;
 691                                         for(int i=0;i<alnLength;i++){
 692                                                 if(temp[i] != '-'){
 693                                                         minPos++;
 694                                                 }
 695                                         }
 696                                 }
 697                                 else if(numDiff == minDiff){
 698                                         minCount++;
 699                                 }
 700
 701                         }
 702                         if(minDiff > bdiffs){   success =  bdiffs + 1;  }
 703                         else if(minCount > 1)   {       success =  bdiffs + 1;  }
 704                         else{
 705                                 group = minGroup;
 706                                 seq.setUnaligned("*" + rawSequence.substr(minPos));
 707                                 success = minDiff;
 708                         }
 709
 710                         if (alignment != NULL) {  delete alignment;  }
 711
 712                 }
 713                 return success;
 714
 715         }
 716         catch(exception& e) {
 717                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
 718                 exit(1);
 719         }
 720
 721 }
 722
 723 //***************************************************************************************************************
 724
 725 int TrimSeqsCommand::stripForward(Sequence& seq){
 726         try {
 727                 string rawSequence = seq.getUnaligned();
 728                 bool success = pdiffs + 1;      //guilty until proven innocent
 729
 730                 //can you find the primer
 731                 for(int i=0;i<numFPrimers;i++){
 732                         string oligo = forPrimer[i];
 733
 734                         if(rawSequence.length() < oligo.length()){
 735                                 success = pdiffs + 1;
 736                                 break;
 737                         }
 738
 739                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 740                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 741                                 success = 0;
 742                                 break;
 743                         }
 744                 }
 745
 746                 //if you found the barcode or if you don't want to allow for diffs
 747 //              cout << success;
 748                 if ((pdiffs == 0) || (success == 0)) { return success;  }
 749
 750                 else { //try aligning and see if you can find it
 751 //                      cout << endl;
 752
 753                         int maxLength = 0;
 754
 755                         Alignment* alignment;
 756                         if (numFPrimers > 0) {
 757
 758                                 for(int i=0;i<numFPrimers;i++){
 759                                         if(forPrimer[i].length() > maxLength){
 760                                                 maxLength = forPrimer[i].length();
 761                                         }
 762                                 }
 763                                 alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+pdiffs+1));
 764
 765                         }else{ alignment = NULL; }
 766
 767                         //can you find the barcode
 768                         int minDiff = 1e6;
 769                         int minCount = 1;
 770                         int minPos = 0;
 771
 772                         for(int i=0;i<numFPrimers;i++){
 773                                 string oligo = forPrimer[i];
 774
 775                                 if(rawSequence.length() < maxLength){
 776                                         success = pdiffs + 1;
 777                                         break;
 778                                 }
 779
 780                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 781                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 782                                 oligo = alignment->getSeqAAln();
 783                                 string temp = alignment->getSeqBAln();
 784
 785                                 int alnLength = oligo.length();
 786
 787                                 for(int i=oligo.length()-1;i>=0;i--){
 788                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 789                                 }
 790                                 oligo = oligo.substr(0,alnLength);
 791                                 temp = temp.substr(0,alnLength);
 792 //                              cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,alnLength) << " raw aligned = " << temp << endl;
 793                                 cout << seq.getName() << endl;
 794                                 cout << temp << endl;
 795                                 cout << oligo << endl;
 796                                 cout << alnLength << endl;
 797                                 cout << endl;
 798
 799                                 int newStart=0;
 800                                 int numDiff = countDiffs(oligo, temp);
 801                                 if(numDiff < minDiff){
 802                                         minDiff = numDiff;
 803                                         minCount = 1;
 804                                         minPos = 0;
 805                                         for(int i=0;i<alnLength;i++){
 806                                                 if(temp[i] != '-'){
 807                                                         minPos++;
 808                                                 }
 809                                         }
 810                                 }
 811                                 else if(numDiff == minDiff){
 812                                         minCount++;
 813                                 }
 814
 815                         }
 816                         if(minDiff > pdiffs){   success =  pdiffs + 1;  }
 817                         else if(minCount > 1)   {       success =  pdiffs + 1;  }
 818                         else{
 819                                 seq.setUnaligned("*" + rawSequence.substr(minPos));
 820                                 success = minDiff;
 821                         }
 822
 823                         if (alignment != NULL) {  delete alignment;  }
 824
 825                 }
 826                 return success;
 827
 828         }
 829         catch(exception& e) {
 830                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
 831                 exit(1);
 832         }
 833 }
 834
 835 //***************************************************************************************************************
 836
 837 bool TrimSeqsCommand::stripReverse(Sequence& seq){
 838         try {
 839                 string rawSequence = seq.getUnaligned();
 840                 bool success = 0;       //guilty until proven innocent
 841
 842                 for(int i=0;i<numRPrimers;i++){
 843                         string oligo = revPrimer[i];
 844
 845                         if(rawSequence.length() < oligo.length()){
 846                                 success = 0;
 847                                 break;
 848                         }
 849
 850                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 851                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 852                                 success = 1;
 853                                 break;
 854                         }
 855                 }
 856                 return success;
 857
 858         }
 859         catch(exception& e) {
 860                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
 861                 exit(1);
 862         }
 863 }
 864
 865 //***************************************************************************************************************
 866
 867 bool TrimSeqsCommand::cullLength(Sequence& seq){
 868         try {
 869
 870                 int length = seq.getNumBases();
 871                 bool success = 0;       //guilty until proven innocent
 872
 873                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
 874                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
 875                 else                                                                                            {       success = 0;    }
 876
 877                 return success;
 878
 879         }
 880         catch(exception& e) {
 881                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
 882                 exit(1);
 883         }
 884
 885 }
 886
 887 //***************************************************************************************************************
 888
 889 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
 890         try {
 891                 int longHomoP = seq.getLongHomoPolymer();
 892                 bool success = 0;       //guilty until proven innocent
 893
 894                 if(longHomoP <= maxHomoP){      success = 1;    }
 895                 else                                    {       success = 0;    }
 896
 897                 return success;
 898         }
 899         catch(exception& e) {
 900                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
 901                 exit(1);
 902         }
 903
 904 }
 905
 906 //***************************************************************************************************************
 907
 908 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
 909         try {
 910                 int numNs = seq.getAmbigBases();
 911                 bool success = 0;       //guilty until proven innocent
 912
 913                 if(numNs <= maxAmbig)   {       success = 1;    }
 914                 else                                    {       success = 0;    }
 915
 916                 return success;
 917         }
 918         catch(exception& e) {
 919                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
 920                 exit(1);
 921         }
 922
 923 }
 924
 925 //***************************************************************************************************************
 926
 927 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 928         try {
 929                 bool success = 1;
 930                 int length = oligo.length();
 931
 932                 for(int i=0;i<length;i++){
 933
 934                         if(oligo[i] != seq[i]){
 935                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 936                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 937                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 938                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 939                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 940                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 941                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 942                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 943                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 944                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 945                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 946                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 947
 948                                 if(success == 0)        {       break;   }
 949                         }
 950                         else{
 951                                 success = 1;
 952                         }
 953                 }
 954
 955                 return success;
 956         }
 957         catch(exception& e) {
 958                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
 959                 exit(1);
 960         }
 961
 962 }
 963 //***************************************************************************************************************
 964
 965 int TrimSeqsCommand::countDiffs(string oligo, string seq){
 966         try {
 967
 968                 int length = oligo.length();
 969                 int countDiffs = 0;
 970
 971                 for(int i=0;i<length;i++){
 972
 973                         if(oligo[i] != seq[i]){
 974                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
 975                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
 976                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
 977                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
 978                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
 979                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
 980                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
 981                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
 982                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 983                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 984                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
 985                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
 986
 987                         }
 988                 }
 989
 990                 return countDiffs;
 991         }
 992         catch(exception& e) {
 993                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
 994                 exit(1);
 995         }
 996
 997 }
 998 //***************************************************************************************************************
 999
1000 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
1001         try {
1002                 string rawSequence = seq.getUnaligned();
1003                 int seqLength;  // = rawSequence.length();
1004                 string name, temp, temp2;
1005
1006                 qFile >> name >> temp;
1007
1008                 splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
1009                 convert(temp, seqLength); //converts string to int
1010
1011                 if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); }  }
1012                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1013
1014                 int score;
1015                 int end = seqLength;
1016
1017                 for(int i=0;i<seqLength;i++){
1018                         qFile >> score;
1019
1020                         if(score <= qThreshold){
1021                                 end = i;
1022                                 break;
1023                         }
1024                 }
1025                 for(int i=end+1;i<seqLength;i++){
1026                         qFile >> score;
1027                 }
1028
1029                 seq.setUnaligned(rawSequence.substr(0,end));
1030
1031                 return 1;
1032         }
1033         catch(exception& e) {
1034                 m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1035                 exit(1);
1036         }
1037 }
1038
1039 //***************************************************************************************************************
1040
1041 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1042         try {
1043                 string rawSequence = seq.getUnaligned();
1044                 int seqLength = seq.getNumBases();
1045                 bool success = 0;       //guilty until proven innocent
1046                 string name;
1047
1048                 qFile >> name;
1049                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1050
1051                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1052
1053                 float score;
1054                 float average = 0;
1055
1056                 for(int i=0;i<seqLength;i++){
1057                         qFile >> score;
1058                         average += score;
1059                 }
1060                 average /= seqLength;
1061
1062                 if(average >= qAverage) {       success = 1;    }
1063                 else                                    {       success = 0;    }
1064
1065                 return success;
1066         }
1067         catch(exception& e) {
1068                 m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1069                 exit(1);
1070         }
1071 }
1072
1073 //***************************************************************************************************************