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                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { temp = "0"; }
 108                         convert(temp, tdiffs);
 109
 110                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found") { temp = "0"; }
 111                         convert(temp, bdiffs);
 112
 113                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 114                         convert(temp, pdiffs);
 115
 116                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 117
 118                         temp = validParameter.validFile(parameters, "qfile", true);
 119                         if (temp == "not found")        {       qFileName = "";         }
 120                         else if(temp == "not open")     {       abort = true;           }
 121                         else                                            {       qFileName = temp;       }
 122
 123                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 124                         convert(temp, qThreshold);
 125
 126                         temp = validParameter.validFile(parameters, "qtrim", false);    if (temp == "not found") { temp = "F"; }
 127                         qtrim = isTrue(temp);
 128
 129                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 130                         convert(temp, qAverage);
 131
 132                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 133                         allFiles = isTrue(temp);
 134
 135                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 136                         convert(temp, processors);
 137
 138                         if(allFiles && oligoFile == ""){
 139                                 m->mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); m->mothurOutEndLine();
 140                         }
 141                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 142                                 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 143                                 qAverage=0;
 144                                 qThreshold=0;
 145                         }
 146                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 147                                 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 148                                 abort = true;
 149                         }
 150                 }
 151
 152         }
 153         catch(exception& e) {
 154                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 155                 exit(1);
 156         }
 157 }
 158 //**********************************************************************************************************************
 159
 160 void TrimSeqsCommand::help(){
 161         try {
 162                 m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 163                 m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 164                 m->mothurOut("The fasta parameter is required.\n");
 165                 m->mothurOut("The flip parameter .... The default is 0.\n");
 166                 m->mothurOut("The oligos parameter .... The default is "".\n");
 167                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 168                 m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 169                 m->mothurOut("The minlength parameter .... The default is 0.\n");
 170                 m->mothurOut("The maxlength parameter .... The default is 0.\n");
 171                 m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is 0.\n");
 172                 m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
 173                 m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
 174                 m->mothurOut("The qfile parameter .....\n");
 175                 m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 176                 m->mothurOut("The qaverage parameter .... The default is 0.\n");
 177                 m->mothurOut("The allfiles parameter .... The default is F.\n");
 178                 m->mothurOut("The qtrim parameter .... The default is F.\n");
 179                 m->mothurOut("The trim.seqs command should be in the following format: \n");
 180                 m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
 181                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 182                 m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 183                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
 184                 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 185
 186         }
 187         catch(exception& e) {
 188                 m->errorOut(e, "TrimSeqsCommand", "help");
 189                 exit(1);
 190         }
 191 }
 192
 193
 194 //***************************************************************************************************************
 195
 196 TrimSeqsCommand::~TrimSeqsCommand(){    /*      do nothing      */      }
 197
 198 //***************************************************************************************************************
 199
 200 int TrimSeqsCommand::execute(){
 201         try{
 202
 203                 if (abort == true) { return 0; }
 204
 205                 numFPrimers = 0;  //this needs to be initialized
 206                 numRPrimers = 0;
 207
 208                 string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
 209                 outputNames.push_back(trimSeqFile);
 210                 string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
 211                 outputNames.push_back(scrapSeqFile);
 212                 string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
 213
 214                 vector<string> fastaFileNames;
 215                 if(oligoFile != ""){
 216                         outputNames.push_back(groupFile);
 217                         getOligos(fastaFileNames);
 218                 }
 219
 220                 if(qFileName != "")     {       setLines(qFileName, qLines);    }
 221
 222
 223                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 224                                 if(processors == 1){
 225                                         ifstream inFASTA;
 226                                         openInputFile(fastaFile, inFASTA);
 227                                         int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 228                                         inFASTA.close();
 229
 230                                         lines.push_back(new linePair(0, numSeqs));
 231
 232                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 233
 234                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 235                                                 rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
 236                                         }
 237
 238                                 }else{
 239                                         setLines(fastaFile, lines);
 240                                         if(qFileName == "")     {       qLines = lines; }
 241
 242                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames);
 243
 244                                         rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
 245                                         rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
 246                                         rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
 247                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 248                                                 rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
 249                                         }
 250                                         //append files
 251                                         for(int i=1;i<processors;i++){
 252                                                 appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
 253                                                 remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
 254                                                 appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
 255                                                 remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
 256                                                 appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 257                                                 remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 258                                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 259                                                         appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
 260                                                         remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 261                                                 }
 262                                         }
 263                                 }
 264
 265                                 if (m->control_pressed) {  return 0; }
 266                 #else
 267                                 ifstream inFASTA;
 268                                 openInputFile(fastafileNames[s], inFASTA);
 269                                 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 270                                 inFASTA.close();
 271
 272                                 lines.push_back(new linePair(0, numSeqs));
 273
 274                                 driverCreateSummary(fastafile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 275
 276                                 if (m->control_pressed) {  return 0; }
 277                 #endif
 278
 279
 280                 for(int i=0;i<fastaFileNames.size();i++){
 281                         ifstream inFASTA;
 282                         string seqName;
 283                         openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
 284                         ofstream outGroups;
 285                         openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
 286                         outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
 287
 288                         while(!inFASTA.eof()){
 289                                 if(inFASTA.get() == '>'){
 290                                         inFASTA >> seqName;
 291                                         outGroups << seqName << '\t' << groupVector[i] << endl;
 292                                 }
 293                                 while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 294                         }
 295                         outGroups.close();
 296                         inFASTA.close();
 297                 }
 298
 299                 if (m->control_pressed) {
 300                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 301                         return 0;
 302                 }
 303
 304                 m->mothurOutEndLine();
 305                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 306                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 307                 m->mothurOutEndLine();
 308
 309                 return 0;
 310
 311         }
 312         catch(exception& e) {
 313                 m->errorOut(e, "TrimSeqsCommand", "execute");
 314                 exit(1);
 315         }
 316 }
 317
 318 /**************************************************************************************/
 319 int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames, linePair* line, linePair* qline) {
 320         try {
 321
 322                 ofstream outFASTA;
 323                 int able = openOutputFile(trimFile, outFASTA);
 324
 325                 ofstream scrapFASTA;
 326                 openOutputFile(scrapFile, scrapFASTA);
 327
 328                 ofstream outGroups;
 329                 vector<ofstream*> fastaFileNames;
 330                 if (oligoFile != "") {
 331                         openOutputFile(groupFile, outGroups);
 332                         for (int i = 0; i < fastaNames.size(); i++) {
 333                                 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 334                         }
 335                 }
 336
 337                 ifstream inFASTA;
 338                 openInputFile(filename, inFASTA);
 339
 340                 ifstream qFile;
 341                 if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
 342
 343                 qFile.seekg(qline->start);
 344                 inFASTA.seekg(line->start);
 345
 346                 for(int i=0;i<line->num;i++){
 347
 348                         if (m->control_pressed) {
 349                                 inFASTA.close();
 350                                 outFASTA.close();
 351                                 scrapFASTA.close();
 352                                 if (oligoFile != "") {   outGroups.close();   }
 353                                 if(qFileName != "")     {       qFile.close();  }
 354                                 for(int i=0;i<fastaFileNames.size();i++){
 355                                         fastaFileNames[i]->close();
 356                                         delete fastaFileNames[i];
 357                                 }
 358                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 359                                 return 0;
 360                         }
 361
 362                         bool success = 1;
 363
 364                         Sequence currSeq(inFASTA);
 365
 366                         string origSeq = currSeq.getUnaligned();
 367                         if (origSeq != "") {
 368                                 int group;
 369                                 string trashCode = "";
 370                                 int currentSeqsDiffs = 0;
 371                                 currentSeqsTdiffs = 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){   trashCode += 'b';       }
 386                                         else{ currentSeqsDiffs += currentSeqsTdiffs;  }
 387                                 }
 388
 389                                 if(numFPrimers != 0){
 390                                         success = stripForward(currSeq);
 391                                         if(!success){   trashCode += 'f';       }
 392                                         else{ currentSeqsDiffs += currentSeqsTdiffs;  }
 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 bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 608         try {
 609                 string rawSequence = seq.getUnaligned();
 610                 bool success = 0;       //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 = 0;
 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 = 1;
 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 == 1)) { 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 = 0;
 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);//, alnLength, newStart, bdiffs);
 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 = 0;    }
 703                         else if(minCount > 1)   {       success = 0;    }
 704                         else{
 705                                 group = minGroup;
 706                                 seq.setUnaligned("*" + rawSequence.substr(minPos));
 707                                 success = 1;
 708                         }
 709
 710                         if (alignment != NULL) {  delete alignment;  }
 711                 }
 712                 return success;
 713
 714         }
 715         catch(exception& e) {
 716                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
 717                 exit(1);
 718         }
 719
 720 }
 721
 722 //***************************************************************************************************************
 723
 724 bool TrimSeqsCommand::stripForward(Sequence& seq){
 725         try {
 726                 string rawSequence = seq.getUnaligned();
 727                 bool success = 0;       //guilty until proven innocent
 728
 729                 for(int i=0;i<numFPrimers;i++){
 730                         string oligo = forPrimer[i];
 731
 732                         if(rawSequence.length() < oligo.length()){
 733                                 success = 0;
 734                                 break;
 735                         }
 736
 737                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 738                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 739                                 success = 1;
 740                                 break;
 741                         }
 742                 }
 743
 744                 //if you found the primer or if you don't want to allow for diffs
 745                 if ((pdiffs == 0) || (success == 1)) { return success;  }
 746
 747                 else { //try aligning and see if you can find it
 748
 749                         Alignment* alignment;
 750                         if (numFPrimers > 0) {  alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (forPrimer[0].length()+pdiffs+1));  }
 751                         else{ alignment = NULL; }
 752                         //can you find the primer
 753                         for(int i=0;i<numFPrimers;i++){
 754                                 string oligo = forPrimer[i];
 755                                 int length = oligo.length();
 756
 757                                 if(rawSequence.length() < oligo.length()){
 758                                         success = 0;
 759                                         break;
 760                                 }
 761
 762                                 //resize if neccessary
 763                                 if ((length+pdiffs+1) > alignment->getnRows()) { alignment->resize(length+pdiffs+1);    }
 764
 765                                 //use needleman to align first primer.length()+numdiffs of sequence to each primer
 766                                 alignment->align(oligo, rawSequence.substr(0,length+pdiffs));
 767                                 oligo = alignment->getSeqAAln();
 768                                 string temp = alignment->getSeqBAln();
 769
 770                                 int newStart = 0;
 771 //                              if(compareDNASeq(oligo, temp, length, newStart, pdiffs)){
 772 //                                      seq.setUnaligned(rawSequence.substr(newStart));
 773 //                                      success = 1;
 774 //                                      break;
 775 //                              }
 776                         }
 777
 778                         if (alignment != NULL) {  delete alignment;  }
 779                 }
 780
 781                 return success;
 782
 783         }
 784         catch(exception& e) {
 785                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
 786                 exit(1);
 787         }
 788 }
 789
 790 //***************************************************************************************************************
 791
 792 bool TrimSeqsCommand::stripReverse(Sequence& seq){
 793         try {
 794                 string rawSequence = seq.getUnaligned();
 795                 bool success = 0;       //guilty until proven innocent
 796
 797                 for(int i=0;i<numRPrimers;i++){
 798                         string oligo = revPrimer[i];
 799
 800                         if(rawSequence.length() < oligo.length()){
 801                                 success = 0;
 802                                 break;
 803                         }
 804
 805                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 806                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 807                                 success = 1;
 808                                 break;
 809                         }
 810                 }
 811                 return success;
 812
 813         }
 814         catch(exception& e) {
 815                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
 816                 exit(1);
 817         }
 818 }
 819
 820 //***************************************************************************************************************
 821
 822 bool TrimSeqsCommand::cullLength(Sequence& seq){
 823         try {
 824
 825                 int length = seq.getNumBases();
 826                 bool success = 0;       //guilty until proven innocent
 827
 828                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
 829                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
 830                 else                                                                                            {       success = 0;    }
 831
 832                 return success;
 833
 834         }
 835         catch(exception& e) {
 836                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
 837                 exit(1);
 838         }
 839
 840 }
 841
 842 //***************************************************************************************************************
 843
 844 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
 845         try {
 846                 int longHomoP = seq.getLongHomoPolymer();
 847                 bool success = 0;       //guilty until proven innocent
 848
 849                 if(longHomoP <= maxHomoP){      success = 1;    }
 850                 else                                    {       success = 0;    }
 851
 852                 return success;
 853         }
 854         catch(exception& e) {
 855                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
 856                 exit(1);
 857         }
 858
 859 }
 860
 861 //***************************************************************************************************************
 862
 863 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
 864         try {
 865                 int numNs = seq.getAmbigBases();
 866                 bool success = 0;       //guilty until proven innocent
 867
 868                 if(numNs <= maxAmbig)   {       success = 1;    }
 869                 else                                    {       success = 0;    }
 870
 871                 return success;
 872         }
 873         catch(exception& e) {
 874                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
 875                 exit(1);
 876         }
 877
 878 }
 879
 880 //***************************************************************************************************************
 881
 882 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 883         try {
 884                 bool success = 1;
 885                 int length = oligo.length();
 886
 887                 for(int i=0;i<length;i++){
 888
 889                         if(oligo[i] != seq[i]){
 890                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 891                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 892                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 893                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 894                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 895                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 896                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 897                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 898                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 899                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 900                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 901                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 902
 903                                 if(success == 0)        {       break;   }
 904                         }
 905                         else{
 906                                 success = 1;
 907                         }
 908                 }
 909
 910                 return success;
 911         }
 912         catch(exception& e) {
 913                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
 914                 exit(1);
 915         }
 916
 917 }
 918 //***************************************************************************************************************
 919
 920 int TrimSeqsCommand::countDiffs(string oligo, string seq){//, int numBases, int& end, int diffs){
 921         try {
 922 //              bool success = 1;
 923                 int length = oligo.length();
 924 //              end = numBases;
 925 //              int countBases = 0;
 926                 int countDiffs = 0;
 927
 928
 929 //              if (length != 0) {
 930 //                      if ((oligo[0] == '-') || (oligo[0] == '.')) {  return 1e6;  } //no gaps allowed at beginning
 931 //              }
 932
 933                 for(int i=0;i<length;i++){
 934
 935 //                      if ((oligo[i] != '-') && (oligo[i] != '.'))  { countBases++; }
 936
 937                         if(oligo[i] != seq[i]){
 938                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
 939                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
 940                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
 941                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
 942                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
 943                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
 944                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
 945                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
 946                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 947                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 948                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
 949                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
 950
 951 //                              if(countDiffs > diffs)  {       break;   }
 952                         }
 953 //                      else{
 954 //                              success = 1;
 955 //                      }
 956
 957 //                      if (countBases >= numBases) { end = countBases; break; } //stop checking after end of barcode or primer
 958                 }
 959                 //if it's a success we want to check for total diffs in driver, so save it.
 960 //              if (success == 1) {  currentSeqsTdiffs = countDiffs; }
 961
 962                 return countDiffs;
 963         }
 964         catch(exception& e) {
 965                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
 966                 exit(1);
 967         }
 968
 969 }
 970 //***************************************************************************************************************
 971
 972 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
 973         try {
 974                 string rawSequence = seq.getUnaligned();
 975                 int seqLength;  // = rawSequence.length();
 976                 string name, temp, temp2;
 977
 978                 qFile >> name >> temp;
 979
 980                 splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
 981                 convert(temp, seqLength); //converts string to int
 982
 983                 if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); }  }
 984                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
 985
 986                 int score;
 987                 int end = seqLength;
 988
 989                 for(int i=0;i<seqLength;i++){
 990                         qFile >> score;
 991
 992                         if(score <= qThreshold){
 993                                 end = i;
 994                                 break;
 995                         }
 996                 }
 997                 for(int i=end+1;i<seqLength;i++){
 998                         qFile >> score;
 999                 }
1000
1001                 seq.setUnaligned(rawSequence.substr(0,end));
1002
1003                 return 1;
1004         }
1005         catch(exception& e) {
1006                 m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1007                 exit(1);
1008         }
1009 }
1010
1011 //***************************************************************************************************************
1012
1013 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1014         try {
1015                 string rawSequence = seq.getUnaligned();
1016                 int seqLength = seq.getNumBases();
1017                 bool success = 0;       //guilty until proven innocent
1018                 string name;
1019
1020                 qFile >> name;
1021                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1022
1023                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1024
1025                 float score;
1026                 float average = 0;
1027
1028                 for(int i=0;i<seqLength;i++){
1029                         qFile >> score;
1030                         average += score;
1031                 }
1032                 average /= seqLength;
1033
1034                 if(average >= qAverage) {       success = 1;    }
1035                 else                                    {       success = 0;    }
1036
1037                 return success;
1038         }
1039         catch(exception& e) {
1040                 m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1041                 exit(1);
1042         }
1043 }
1044
1045 //***************************************************************************************************************