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 will output the reverse compliment of your trimmed sequence. The default is false.\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                                         int numSeqs;
 228                                         openInputFile(fastaFile, inFASTA);
 229                                         getNumSeqs(inFASTA, numSeqs);
 230                                         inFASTA.close();
 231
 232                                         lines.push_back(new linePair(0, numSeqs));
 233
 234                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 235
 236                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 237                                                 rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
 238                                         }
 239
 240                                 }else{
 241                                         setLines(fastaFile, lines);
 242                                         if(qFileName == "")     {       qLines = lines; }
 243
 244                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames);
 245
 246                                         rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
 247                                         rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
 248                                         rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
 249                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 250                                                 rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
 251                                         }
 252                                         //append files
 253                                         for(int i=1;i<processors;i++){
 254                                                 appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
 255                                                 remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
 256                                                 appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
 257                                                 remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
 258                                                 appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 259                                                 remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 260                                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 261                                                         appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
 262                                                         remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 263                                                 }
 264                                         }
 265                                 }
 266
 267                                 if (m->control_pressed) {  return 0; }
 268                 #else
 269                                 ifstream inFASTA;
 270                                 int numSeqs;
 271                                 openInputFile(fastaFile, inFASTA);
 272                                 getNumSeqs(inFASTA, numSeqs);
 273                                 inFASTA.close();
 274
 275                                 lines.push_back(new linePair(0, numSeqs));
 276
 277                                 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 278
 279                                 if (m->control_pressed) {  return 0; }
 280                 #endif
 281
 282
 283                 for(int i=0;i<fastaFileNames.size();i++){
 284                         ifstream inFASTA;
 285                         string seqName;
 286                         openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
 287                         ofstream outGroups;
 288                         openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
 289                         outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
 290
 291                         while(!inFASTA.eof()){
 292                                 if(inFASTA.get() == '>'){
 293                                         inFASTA >> seqName;
 294                                         outGroups << seqName << '\t' << groupVector[i] << endl;
 295                                 }
 296                                 while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 297                         }
 298                         outGroups.close();
 299                         inFASTA.close();
 300                 }
 301
 302                 if (m->control_pressed) {
 303                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 304                         return 0;
 305                 }
 306
 307                 m->mothurOutEndLine();
 308                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 309                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 310                 m->mothurOutEndLine();
 311
 312                 return 0;
 313
 314         }
 315         catch(exception& e) {
 316                 m->errorOut(e, "TrimSeqsCommand", "execute");
 317                 exit(1);
 318         }
 319 }
 320
 321 /**************************************************************************************/
 322 int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames, linePair* line, linePair* qline) {
 323         try {
 324
 325                 ofstream outFASTA;
 326                 int able = openOutputFile(trimFile, outFASTA);
 327
 328                 ofstream scrapFASTA;
 329                 openOutputFile(scrapFile, scrapFASTA);
 330
 331                 ofstream outGroups;
 332                 vector<ofstream*> fastaFileNames;
 333                 if (oligoFile != "") {
 334                         openOutputFile(groupFile, outGroups);
 335                         for (int i = 0; i < fastaNames.size(); i++) {
 336                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 337                                 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 338                         #else
 339                                 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
 340                         #endif
 341                         }
 342                 }
 343
 344                 ifstream inFASTA;
 345                 openInputFile(filename, inFASTA);
 346
 347                 ifstream qFile;
 348                 if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
 349
 350                 qFile.seekg(qline->start);
 351                 inFASTA.seekg(line->start);
 352
 353                 for(int i=0;i<line->num;i++){
 354
 355                         if (m->control_pressed) {
 356                                 inFASTA.close();
 357                                 outFASTA.close();
 358                                 scrapFASTA.close();
 359                                 if (oligoFile != "") {   outGroups.close();   }
 360                                 if(qFileName != "")     {       qFile.close();  }
 361                                 for(int i=0;i<fastaFileNames.size();i++){
 362                                         fastaFileNames[i]->close();
 363                                         delete fastaFileNames[i];
 364                                 }
 365                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 366                                 return 0;
 367                         }
 368
 369                         int success = 1;
 370
 371                         Sequence currSeq(inFASTA);
 372
 373                         string origSeq = currSeq.getUnaligned();
 374                         if (origSeq != "") {
 375                                 int group;
 376                                 string trashCode = "";
 377                                 int currentSeqsDiffs = 0;
 378
 379                                 if(qFileName != ""){
 380                                         if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
 381                                         else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
 382
 383                                         if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
 384                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 385                                         }
 386
 387                                         if(!success)                    {       trashCode += 'q';                                                               }
 388                                 }
 389
 390                                 if(barcodes.size() != 0){
 391                                         success = stripBarcode(currSeq, group);
 392                                         if(success > bdiffs){   trashCode += 'b';       }
 393                                         else{ currentSeqsDiffs += success;  }
 394                                 }
 395
 396                                 if(numFPrimers != 0){
 397                                         success = stripForward(currSeq);
 398                                         if(success > pdiffs){   trashCode += 'f';       }
 399                                         else{ currentSeqsDiffs += success;  }
 400                                 }
 401
 402                                 if (currentSeqsDiffs > tdiffs) { trashCode += 't';   }
 403
 404                                 if(numRPrimers != 0){
 405                                         success = stripReverse(currSeq);
 406                                         if(!success){   trashCode += 'r';       }
 407                                 }
 408
 409                                 if(minLength > 0 || maxLength > 0){
 410                                         success = cullLength(currSeq);
 411                                         if(!success){   trashCode += 'l'; }
 412                                 }
 413                                 if(maxHomoP > 0){
 414                                         success = cullHomoP(currSeq);
 415                                         if(!success){   trashCode += 'h';       }
 416                                 }
 417                                 if(maxAmbig != -1){
 418                                         success = cullAmbigs(currSeq);
 419                                         if(!success){   trashCode += 'n';       }
 420                                 }
 421
 422                                 if(flip){       currSeq.reverseComplement();    }               // should go last
 423
 424                                 if(trashCode.length() == 0){
 425                                         currSeq.setAligned(currSeq.getUnaligned());
 426                                         currSeq.printSequence(outFASTA);
 427                                         if(barcodes.size() != 0){
 428                                                 outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
 429
 430                                                 if(allFiles){
 431                                                         currSeq.printSequence(*fastaFileNames[group]);
 432                                                 }
 433                                         }
 434                                 }
 435                                 else{
 436                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 437                                         currSeq.setUnaligned(origSeq);
 438                                         currSeq.setAligned(origSeq);
 439                                         currSeq.printSequence(scrapFASTA);
 440                                 }
 441                         }
 442                         gobble(inFASTA);
 443                 }
 444
 445                 inFASTA.close();
 446                 outFASTA.close();
 447                 scrapFASTA.close();
 448                 if (oligoFile != "") {   outGroups.close();   }
 449                 if(qFileName != "")     {       qFile.close();  }
 450
 451                 for(int i=0;i<fastaFileNames.size();i++){
 452                         fastaFileNames[i]->close();
 453                         delete fastaFileNames[i];
 454                 }
 455
 456                 return 0;
 457         }
 458         catch(exception& e) {
 459                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 460                 exit(1);
 461         }
 462 }
 463 /**************************************************************************************************/
 464 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames) {
 465         try {
 466 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 467                 int process = 0;
 468                 int exitCommand = 1;
 469                 processIDS.clear();
 470
 471                 //loop through and create all the processes you want
 472                 while (process != processors) {
 473                         int pid = fork();
 474
 475                         if (pid > 0) {
 476                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 477                                 process++;
 478                         }else if (pid == 0){
 479                                 driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, lines[process], qLines[process]);
 480                                 exit(0);
 481                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 482                 }
 483
 484                 //force parent to wait until all the processes are done
 485                 for (int i=0;i<processors;i++) {
 486                         int temp = processIDS[i];
 487                         wait(&temp);
 488                 }
 489
 490                 return exitCommand;
 491 #endif
 492         }
 493         catch(exception& e) {
 494                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 495                 exit(1);
 496         }
 497 }
 498 /**************************************************************************************************/
 499
 500 int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
 501         try {
 502
 503                 lines.clear();
 504
 505                 vector<long int> positions;
 506
 507                 ifstream inFASTA;
 508                 openInputFile(filename, inFASTA);
 509
 510                 string input;
 511                 while(!inFASTA.eof()){
 512                         input = getline(inFASTA);
 513
 514                         if (input.length() != 0) {
 515                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 516                         }
 517                 }
 518                 inFASTA.close();
 519
 520                 int numFastaSeqs = positions.size();
 521
 522                 FILE * pFile;
 523                 long size;
 524
 525                 //get num bytes in file
 526                 pFile = fopen (filename.c_str(),"rb");
 527                 if (pFile==NULL) perror ("Error opening file");
 528                 else{
 529                         fseek (pFile, 0, SEEK_END);
 530                         size=ftell (pFile);
 531                         fclose (pFile);
 532                 }
 533
 534                 int numSeqsPerProcessor = numFastaSeqs / processors;
 535
 536                 for (int i = 0; i < processors; i++) {
 537
 538                         long int startPos = positions[ i * numSeqsPerProcessor ];
 539                         if(i == processors - 1){
 540                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 541                         }else{
 542                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 543                         }
 544                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 545                 }
 546
 547                 return numFastaSeqs;
 548         }
 549         catch(exception& e) {
 550                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 551                 exit(1);
 552         }
 553 }
 554 //***************************************************************************************************************
 555
 556 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*>& outFASTAVec
 557         try {
 558                 ifstream inOligos;
 559                 openInputFile(oligoFile, inOligos);
 560
 561                 ofstream test;
 562
 563                 string type, oligo, group;
 564                 int index=0;
 565
 566                 while(!inOligos.eof()){
 567                         inOligos >> type;
 568
 569                         if(type[0] == '#'){
 570                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 571                         }
 572                         else{
 573                                 inOligos >> oligo;
 574
 575                                 for(int i=0;i<oligo.length();i++){
 576                                         oligo[i] = toupper(oligo[i]);
 577                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 578                                 }
 579
 580                                 if(type == "forward"){
 581                                         forPrimer.push_back(oligo);
 582                                 }
 583                                 else if(type == "reverse"){
 584                                         Sequence oligoRC("reverse", oligo);
 585                                         oligoRC.reverseComplement();
 586                                         revPrimer.push_back(oligoRC.getUnaligned());
 587                                 }
 588                                 else if(type == "barcode"){
 589                                         inOligos >> group;
 590                                         barcodes[oligo]=index++;
 591                                         groupVector.push_back(group);
 592
 593                                         if(allFiles){
 594                                                 //outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
 595                                                 outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 596                                                 outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 597                                         }
 598                                 }
 599                         }
 600                 }
 601
 602                 inOligos.close();
 603
 604                 numFPrimers = forPrimer.size();
 605                 numRPrimers = revPrimer.size();
 606
 607         }
 608         catch(exception& e) {
 609                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 610                 exit(1);
 611         }
 612 }
 613 //***************************************************************************************************************
 614
 615 int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 616         try {
 617
 618                 string rawSequence = seq.getUnaligned();
 619                 int success = bdiffs + 1;       //guilty until proven innocent
 620
 621                 //can you find the barcode
 622                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 623                         string oligo = it->first;
 624                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 625                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 626                                 break;
 627                         }
 628
 629                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 630                                 group = it->second;
 631                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 632                                 success = 0;
 633                                 break;
 634                         }
 635                 }
 636
 637                 //if you found the barcode or if you don't want to allow for diffs
 638 //              cout << success;
 639                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 640
 641                 else { //try aligning and see if you can find it
 642 //                      cout << endl;
 643
 644                         int maxLength = 0;
 645
 646                         Alignment* alignment;
 647                         if (barcodes.size() > 0) {
 648                                 map<string,int>::iterator it=barcodes.begin();
 649
 650                                 for(it;it!=barcodes.end();it++){
 651                                         if(it->first.length() > maxLength){
 652                                                 maxLength = it->first.length();
 653                                         }
 654                                 }
 655                                 alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+bdiffs+1));
 656
 657                         }else{ alignment = NULL; }
 658
 659                         //can you find the barcode
 660                         int minDiff = 1e6;
 661                         int minCount = 1;
 662                         int minGroup = -1;
 663                         int minPos = 0;
 664
 665                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 666                                 string oligo = it->first;
 667 //                              int length = oligo.length();
 668
 669                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 670                                         success = bdiffs + 10;
 671                                         break;
 672                                 }
 673
 674                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 675                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 676                                 oligo = alignment->getSeqAAln();
 677                                 string temp = alignment->getSeqBAln();
 678
 679                                 int alnLength = oligo.length();
 680
 681                                 for(int i=oligo.length()-1;i>=0;i--){
 682                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 683                                 }
 684                                 oligo = oligo.substr(0,alnLength);
 685                                 temp = temp.substr(0,alnLength);
 686
 687                                 int newStart=0;
 688                                 int numDiff = countDiffs(oligo, temp);
 689                                 if(numDiff < minDiff){
 690                                         minDiff = numDiff;
 691                                         minCount = 1;
 692                                         minGroup = it->second;
 693                                         minPos = 0;
 694                                         for(int i=0;i<alnLength;i++){
 695                                                 if(temp[i] != '-'){
 696                                                         minPos++;
 697                                                 }
 698                                         }
 699                                 }
 700                                 else if(numDiff == minDiff){
 701                                         minCount++;
 702                                 }
 703
 704                         }
 705
 706                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
 707                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
 708                         else{                                                                                                   //use the best match
 709                                 group = minGroup;
 710                                 seq.setUnaligned(rawSequence.substr(minPos));
 711                                 success = minDiff;
 712                         }
 713
 714                         if (alignment != NULL) {  delete alignment;  }
 715
 716                 }
 717 //              cout << success << endl;
 718
 719                 return success;
 720
 721         }
 722         catch(exception& e) {
 723                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
 724                 exit(1);
 725         }
 726
 727 }
 728
 729 //***************************************************************************************************************
 730
 731 int TrimSeqsCommand::stripForward(Sequence& seq){
 732         try {
 733                 string rawSequence = seq.getUnaligned();
 734                 int success = pdiffs + 1;       //guilty until proven innocent
 735
 736                 //can you find the primer
 737                 for(int i=0;i<numFPrimers;i++){
 738                         string oligo = forPrimer[i];
 739
 740                         if(rawSequence.length() < oligo.length()){
 741                                 success = pdiffs + 1;
 742                                 break;
 743                         }
 744
 745                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 746                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 747                                 success = 0;
 748                                 break;
 749                         }
 750                 }
 751
 752                 //if you found the barcode or if you don't want to allow for diffs
 753 //              cout << success;
 754                 if ((pdiffs == 0) || (success == 0)) { return success;  }
 755
 756                 else { //try aligning and see if you can find it
 757 //                      cout << endl;
 758
 759                         int maxLength = 0;
 760
 761                         Alignment* alignment;
 762                         if (numFPrimers > 0) {
 763
 764                                 for(int i=0;i<numFPrimers;i++){
 765                                         if(forPrimer[i].length() > maxLength){
 766                                                 maxLength = forPrimer[i].length();
 767                                         }
 768                                 }
 769                                 alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+pdiffs+1));
 770
 771                         }else{ alignment = NULL; }
 772
 773                         //can you find the barcode
 774                         int minDiff = 1e6;
 775                         int minCount = 1;
 776                         int minPos = 0;
 777
 778                         for(int i=0;i<numFPrimers;i++){
 779                                 string oligo = forPrimer[i];
 780
 781                                 if(rawSequence.length() < maxLength){
 782                                         success = pdiffs + 100;
 783                                         break;
 784                                 }
 785
 786                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 787                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 788                                 oligo = alignment->getSeqAAln();
 789                                 string temp = alignment->getSeqBAln();
 790
 791                                 int alnLength = oligo.length();
 792
 793                                 for(int i=oligo.length()-1;i>=0;i--){
 794                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 795                                 }
 796                                 oligo = oligo.substr(0,alnLength);
 797                                 temp = temp.substr(0,alnLength);
 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 =  minDiff;             }
 817                         else if(minCount > 1)   {       success =  pdiffs + 10; }
 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;
1007 //
1008 //              //get rest of line
1009 //              temp = "";
1010 //              while (!qFile.eof())    {
1011 //                      char c = qFile.get();
1012 //                      if (c == 10 || c == 13){        break;  }
1013 //                      else { temp += c; }
1014 //              }
1015 //
1016 //              int pos = temp.find("length");
1017 //              if (pos == temp.npos) { m->mothurOut("Cannot find length in qfile for " + seq.getName()); m->mothurOutEndLine();  seqLength = 0;  }
1018 //              else {
1019 //                      string tempLength = temp.substr(pos);
1020 //                      istringstream iss (tempLength,istringstream::in);
1021 //                      iss >> temp;
1022 //              }
1023 //
1024 //              splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
1025 //              convert(temp, seqLength); //converts string to int
1026 //
1027 //              if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); }  }
1028
1029                 string rawSequence = seq.getUnaligned();
1030                 int seqLength = seq.getNumBases();
1031                 bool success = 0;       //guilty until proven innocent
1032                 string name;
1033
1034                 qFile >> name;
1035                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1036
1037                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1038
1039                 int score;
1040                 int end = seqLength;
1041
1042                 for(int i=0;i<seqLength;i++){
1043                         qFile >> score;
1044
1045                         if(score < qThreshold){
1046                                 end = i;
1047                                 break;
1048                         }
1049                 }
1050                 for(int i=end+1;i<seqLength;i++){
1051                         qFile >> score;
1052                 }
1053
1054                 seq.setUnaligned(rawSequence.substr(0,end));
1055
1056                 return 1;
1057         }
1058         catch(exception& e) {
1059                 m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1060                 exit(1);
1061         }
1062 }
1063
1064 //***************************************************************************************************************
1065
1066 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1067         try {
1068                 string rawSequence = seq.getUnaligned();
1069                 int seqLength = seq.getNumBases();
1070                 bool success = 0;       //guilty until proven innocent
1071                 string name;
1072
1073                 qFile >> name;
1074                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1075
1076                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1077
1078                 float score;
1079                 float average = 0;
1080
1081                 for(int i=0;i<seqLength;i++){
1082                         qFile >> score;
1083                         average += score;
1084                 }
1085                 average /= seqLength;
1086
1087                 if(average >= qAverage) {       success = 1;    }
1088                 else                                    {       success = 0;    }
1089
1090                 return success;
1091         }
1092         catch(exception& e) {
1093                 m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1094                 exit(1);
1095         }
1096 }
1097
1098 //***************************************************************************************************************