trimseqscommand.cpp

   1 /*
   2  *  trimseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/6/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "trimseqscommand.h"
  11 #include "needlemanoverlap.hpp"
  12
  13 //***************************************************************************************************************
  14
  15 TrimSeqsCommand::TrimSeqsCommand(string option)  {
  16         try {
  17
  18                 abort = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
  26                                                                         "qthreshold", "qaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
  27
  28                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  29
  30                         OptionParser parser(option);
  31                         map<string,string> parameters = parser.getParameters();
  32
  33                         ValidParameters validParameter;
  34                         map<string,string>::iterator it;
  35
  36                         //check to make sure all parameters are valid for command
  37                         for (it = parameters.begin(); it != parameters.end(); it++) {
  38                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  39                         }
  40
  41                         //if the user changes the input directory command factory will send this info to us in the output parameter
  42                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  43                         if (inputDir == "not found"){   inputDir = "";          }
  44                         else {
  45                                 string path;
  46                                 it = parameters.find("fasta");
  47                                 //user has given a template file
  48                                 if(it != parameters.end()){
  49                                         path = hasPath(it->second);
  50                                         //if the user has not given a path then, add inputdir. else leave path alone.
  51                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  52                                 }
  53
  54                                 it = parameters.find("oligos");
  55                                 //user has given a template file
  56                                 if(it != parameters.end()){
  57                                         path = hasPath(it->second);
  58                                         //if the user has not given a path then, add inputdir. else leave path alone.
  59                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
  60                                 }
  61
  62                                 it = parameters.find("qfile");
  63                                 //user has given a template file
  64                                 if(it != parameters.end()){
  65                                         path = hasPath(it->second);
  66                                         //if the user has not given a path then, add inputdir. else leave path alone.
  67                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
  68                                 }
  69                         }
  70
  71
  72                         //check for required parameters
  73                         fastaFile = validParameter.validFile(parameters, "fasta", true);
  74                         if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
  75                         else if (fastaFile == "not open") { abort = true; }
  76
  77                         //if the user changes the output directory command factory will send this info to us in the output parameter
  78                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  79                                 outputDir = "";
  80                                 outputDir += hasPath(fastaFile); //if user entered a file with a path then preserve it
  81                         }
  82
  83                         //check for optional parameter and set defaults
  84                         // ...at some point should added some additional type checking...
  85                         string temp;
  86                         temp = validParameter.validFile(parameters, "flip", false);
  87                         if (temp == "not found"){       flip = 0;       }
  88                         else if(isTrue(temp))   {       flip = 1;       }
  89
  90                         temp = validParameter.validFile(parameters, "oligos", true);
  91                         if (temp == "not found"){       oligoFile = "";         }
  92                         else if(temp == "not open"){    abort = true;   }
  93                         else                                    {       oligoFile = temp;               }
  94
  95                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
  96                         convert(temp, maxAmbig);
  97
  98                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
  99                         convert(temp, maxHomoP);
 100
 101                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
 102                         convert(temp, minLength);
 103
 104                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
 105                         convert(temp, maxLength);
 106
 107
 108                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found") { temp = "0"; }
 109                         convert(temp, bdiffs);
 110
 111                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 112                         convert(temp, pdiffs);
 113
 114                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 115                         convert(temp, tdiffs);
 116
 117                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 118
 119                         temp = validParameter.validFile(parameters, "qfile", true);
 120                         if (temp == "not found")        {       qFileName = "";         }
 121                         else if(temp == "not open")     {       abort = true;           }
 122                         else                                            {       qFileName = temp;       }
 123
 124                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 125                         convert(temp, qThreshold);
 126
 127                         temp = validParameter.validFile(parameters, "qtrim", false);    if (temp == "not found") { temp = "F"; }
 128                         qtrim = isTrue(temp);
 129
 130                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 131                         convert(temp, qAverage);
 132
 133                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 134                         allFiles = isTrue(temp);
 135
 136                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 137                         convert(temp, processors);
 138
 139                         if(allFiles && oligoFile == ""){
 140                                 m->mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); m->mothurOutEndLine();
 141                         }
 142                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 143                                 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 144                                 qAverage=0;
 145                                 qThreshold=0;
 146                         }
 147                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 148                                 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 149                                 abort = true;
 150                         }
 151                 }
 152
 153         }
 154         catch(exception& e) {
 155                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 156                 exit(1);
 157         }
 158 }
 159 //**********************************************************************************************************************
 160
 161 void TrimSeqsCommand::help(){
 162         try {
 163                 m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 164                 m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 165                 m->mothurOut("The fasta parameter is required.\n");
 166                 m->mothurOut("The flip parameter .... The default is 0.\n");
 167                 m->mothurOut("The oligos parameter .... The default is "".\n");
 168                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 169                 m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 170                 m->mothurOut("The minlength parameter .... The default is 0.\n");
 171                 m->mothurOut("The maxlength parameter .... The default is 0.\n");
 172                 m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
 173                 m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
 174                 m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
 175                 m->mothurOut("The qfile parameter .....\n");
 176                 m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 177                 m->mothurOut("The qaverage parameter .... The default is 0.\n");
 178                 m->mothurOut("The allfiles parameter .... The default is F.\n");
 179                 m->mothurOut("The qtrim parameter .... The default is F.\n");
 180                 m->mothurOut("The trim.seqs command should be in the following format: \n");
 181                 m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
 182                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 183                 m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 184                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
 185                 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 186
 187         }
 188         catch(exception& e) {
 189                 m->errorOut(e, "TrimSeqsCommand", "help");
 190                 exit(1);
 191         }
 192 }
 193
 194
 195 //***************************************************************************************************************
 196
 197 TrimSeqsCommand::~TrimSeqsCommand(){    /*      do nothing      */      }
 198
 199 //***************************************************************************************************************
 200
 201 int TrimSeqsCommand::execute(){
 202         try{
 203
 204                 if (abort == true) { return 0; }
 205
 206                 numFPrimers = 0;  //this needs to be initialized
 207                 numRPrimers = 0;
 208
 209                 string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
 210                 outputNames.push_back(trimSeqFile);
 211                 string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
 212                 outputNames.push_back(scrapSeqFile);
 213                 string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
 214
 215                 vector<string> fastaFileNames;
 216                 if(oligoFile != ""){
 217                         outputNames.push_back(groupFile);
 218                         getOligos(fastaFileNames);
 219                 }
 220
 221                 if(qFileName != "")     {       setLines(qFileName, qLines);    }
 222
 223
 224                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 225                                 if(processors == 1){
 226                                         ifstream inFASTA;
 227                                         openInputFile(fastaFile, inFASTA);
 228                                         int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 229                                         inFASTA.close();
 230
 231                                         lines.push_back(new linePair(0, numSeqs));
 232
 233                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 234
 235                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 236                                                 rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
 237                                         }
 238
 239                                 }else{
 240                                         setLines(fastaFile, lines);
 241                                         if(qFileName == "")     {       qLines = lines; }
 242
 243                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames);
 244
 245                                         rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
 246                                         rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
 247                                         rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
 248                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 249                                                 rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
 250                                         }
 251                                         //append files
 252                                         for(int i=1;i<processors;i++){
 253                                                 appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
 254                                                 remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
 255                                                 appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
 256                                                 remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
 257                                                 appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 258                                                 remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 259                                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 260                                                         appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
 261                                                         remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 262                                                 }
 263                                         }
 264                                 }
 265
 266                                 if (m->control_pressed) {  return 0; }
 267                 #else
 268                                 ifstream inFASTA;
 269                                 openInputFile(fastaFile, inFASTA);
 270                                 int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 271                                 inFASTA.close();
 272
 273                                 lines.push_back(new linePair(0, numSeqs));
 274
 275                                 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
 276
 277                                 if (m->control_pressed) {  return 0; }
 278                 #endif
 279
 280
 281                 for(int i=0;i<fastaFileNames.size();i++){
 282                         ifstream inFASTA;
 283                         string seqName;
 284                         openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
 285                         ofstream outGroups;
 286                         openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
 287                         outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
 288
 289                         while(!inFASTA.eof()){
 290                                 if(inFASTA.get() == '>'){
 291                                         inFASTA >> seqName;
 292                                         outGroups << seqName << '\t' << groupVector[i] << endl;
 293                                 }
 294                                 while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 295                         }
 296                         outGroups.close();
 297                         inFASTA.close();
 298                 }
 299
 300                 if (m->control_pressed) {
 301                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 302                         return 0;
 303                 }
 304
 305                 m->mothurOutEndLine();
 306                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 307                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 308                 m->mothurOutEndLine();
 309
 310                 return 0;
 311
 312         }
 313         catch(exception& e) {
 314                 m->errorOut(e, "TrimSeqsCommand", "execute");
 315                 exit(1);
 316         }
 317 }
 318
 319 /**************************************************************************************/
 320 int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames, linePair* line, linePair* qline) {
 321         try {
 322
 323                 ofstream outFASTA;
 324                 int able = openOutputFile(trimFile, outFASTA);
 325
 326                 ofstream scrapFASTA;
 327                 openOutputFile(scrapFile, scrapFASTA);
 328
 329                 ofstream outGroups;
 330                 vector<ofstream*> fastaFileNames;
 331                 if (oligoFile != "") {
 332                         openOutputFile(groupFile, outGroups);
 333                         for (int i = 0; i < fastaNames.size(); i++) {
 334                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 335                                 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 336                         #else
 337                                 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
 338                         #endif
 339                         }
 340                 }
 341
 342                 ifstream inFASTA;
 343                 openInputFile(filename, inFASTA);
 344
 345                 ifstream qFile;
 346                 if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
 347
 348                 qFile.seekg(qline->start);
 349                 inFASTA.seekg(line->start);
 350
 351                 for(int i=0;i<line->num;i++){
 352
 353                         if (m->control_pressed) {
 354                                 inFASTA.close();
 355                                 outFASTA.close();
 356                                 scrapFASTA.close();
 357                                 if (oligoFile != "") {   outGroups.close();   }
 358                                 if(qFileName != "")     {       qFile.close();  }
 359                                 for(int i=0;i<fastaFileNames.size();i++){
 360                                         fastaFileNames[i]->close();
 361                                         delete fastaFileNames[i];
 362                                 }
 363                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 364                                 return 0;
 365                         }
 366
 367                         int success = 1;
 368
 369                         Sequence currSeq(inFASTA);
 370
 371                         string origSeq = currSeq.getUnaligned();
 372                         if (origSeq != "") {
 373                                 int group;
 374                                 string trashCode = "";
 375                                 int currentSeqsDiffs = 0;
 376
 377                                 if(qFileName != ""){
 378                                         if(qThreshold != 0)             {       success = stripQualThreshold(currSeq, qFile);   }
 379                                         else if(qAverage != 0)  {       success = cullQualAverage(currSeq, qFile);              }
 380                                         if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) {
 381                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 382                                         }
 383                                         if(!success)                    {       trashCode += 'q';                                                               }
 384                                 }
 385
 386                                 if(barcodes.size() != 0){
 387                                         success = stripBarcode(currSeq, group);
 388                                         if(success > bdiffs){   trashCode += 'b';       }
 389                                         else{ currentSeqsDiffs += success;  }
 390                                 }
 391
 392                                 if(numFPrimers != 0){
 393                                         success = stripForward(currSeq);
 394                                         if(success > pdiffs){   trashCode += 'f';       }
 395                                         else{ currentSeqsDiffs += success;  }
 396                                 }
 397
 398                                 if (currentSeqsDiffs > tdiffs) { trashCode += 't';   }
 399
 400                                 if(numRPrimers != 0){
 401                                         success = stripReverse(currSeq);
 402                                         if(!success){   trashCode += 'r';       }
 403                                 }
 404
 405                                 if(minLength > 0 || maxLength > 0){
 406                                         success = cullLength(currSeq);
 407                                         if(!success){   trashCode += 'l'; }
 408                                 }
 409                                 if(maxHomoP > 0){
 410                                         success = cullHomoP(currSeq);
 411                                         if(!success){   trashCode += 'h';       }
 412                                 }
 413                                 if(maxAmbig != -1){
 414                                         success = cullAmbigs(currSeq);
 415                                         if(!success){   trashCode += 'n';       }
 416                                 }
 417
 418                                 if(flip){       currSeq.reverseComplement();    }               // should go last
 419
 420                                 if(trashCode.length() == 0){
 421                                         currSeq.setAligned(currSeq.getUnaligned());
 422                                         currSeq.printSequence(outFASTA);
 423                                         if(barcodes.size() != 0){
 424                                                 outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
 425
 426                                                 if(allFiles){
 427                                                         currSeq.printSequence(*fastaFileNames[group]);
 428                                                 }
 429                                         }
 430                                 }
 431                                 else{
 432                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 433                                         currSeq.setUnaligned(origSeq);
 434                                         currSeq.setAligned(origSeq);
 435                                         currSeq.printSequence(scrapFASTA);
 436                                 }
 437                         }
 438                         gobble(inFASTA);
 439                 }
 440
 441                 inFASTA.close();
 442                 outFASTA.close();
 443                 scrapFASTA.close();
 444                 if (oligoFile != "") {   outGroups.close();   }
 445                 if(qFileName != "")     {       qFile.close();  }
 446
 447                 for(int i=0;i<fastaFileNames.size();i++){
 448                         fastaFileNames[i]->close();
 449                         delete fastaFileNames[i];
 450                 }
 451
 452                 return 0;
 453         }
 454         catch(exception& e) {
 455                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 456                 exit(1);
 457         }
 458 }
 459 /**************************************************************************************************/
 460 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames) {
 461         try {
 462 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 463                 int process = 0;
 464                 int exitCommand = 1;
 465                 processIDS.clear();
 466
 467                 //loop through and create all the processes you want
 468                 while (process != processors) {
 469                         int pid = fork();
 470
 471                         if (pid > 0) {
 472                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 473                                 process++;
 474                         }else if (pid == 0){
 475                                 driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, lines[process], qLines[process]);
 476                                 exit(0);
 477                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 478                 }
 479
 480                 //force parent to wait until all the processes are done
 481                 for (int i=0;i<processors;i++) {
 482                         int temp = processIDS[i];
 483                         wait(&temp);
 484                 }
 485
 486                 return exitCommand;
 487 #endif
 488         }
 489         catch(exception& e) {
 490                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 491                 exit(1);
 492         }
 493 }
 494 /**************************************************************************************************/
 495
 496 int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
 497         try {
 498
 499                 lines.clear();
 500
 501                 vector<long int> positions;
 502
 503                 ifstream inFASTA;
 504                 openInputFile(filename, inFASTA);
 505
 506                 string input;
 507                 while(!inFASTA.eof()){
 508                         input = getline(inFASTA);
 509
 510                         if (input.length() != 0) {
 511                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 512                         }
 513                 }
 514                 inFASTA.close();
 515
 516                 int numFastaSeqs = positions.size();
 517
 518                 FILE * pFile;
 519                 long size;
 520
 521                 //get num bytes in file
 522                 pFile = fopen (filename.c_str(),"rb");
 523                 if (pFile==NULL) perror ("Error opening file");
 524                 else{
 525                         fseek (pFile, 0, SEEK_END);
 526                         size=ftell (pFile);
 527                         fclose (pFile);
 528                 }
 529
 530                 int numSeqsPerProcessor = numFastaSeqs / processors;
 531
 532                 for (int i = 0; i < processors; i++) {
 533
 534                         long int startPos = positions[ i * numSeqsPerProcessor ];
 535                         if(i == processors - 1){
 536                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 537                         }else{
 538                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 539                         }
 540                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 541                 }
 542
 543                 return numFastaSeqs;
 544         }
 545         catch(exception& e) {
 546                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 547                 exit(1);
 548         }
 549 }
 550 //***************************************************************************************************************
 551
 552 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*>& outFASTAVec
 553         try {
 554                 ifstream inOligos;
 555                 openInputFile(oligoFile, inOligos);
 556
 557                 ofstream test;
 558
 559                 string type, oligo, group;
 560                 int index=0;
 561
 562                 while(!inOligos.eof()){
 563                         inOligos >> type;
 564
 565                         if(type[0] == '#'){
 566                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 567                         }
 568                         else{
 569                                 inOligos >> oligo;
 570
 571                                 for(int i=0;i<oligo.length();i++){
 572                                         oligo[i] = toupper(oligo[i]);
 573                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 574                                 }
 575
 576                                 if(type == "forward"){
 577                                         forPrimer.push_back(oligo);
 578                                 }
 579                                 else if(type == "reverse"){
 580                                         Sequence oligoRC("reverse", oligo);
 581                                         oligoRC.reverseComplement();
 582                                         revPrimer.push_back(oligoRC.getUnaligned());
 583                                 }
 584                                 else if(type == "barcode"){
 585                                         inOligos >> group;
 586                                         barcodes[oligo]=index++;
 587                                         groupVector.push_back(group);
 588
 589                                         if(allFiles){
 590                                                 //outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
 591                                                 outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 592                                                 outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 593                                         }
 594                                 }
 595                         }
 596                 }
 597
 598                 inOligos.close();
 599
 600                 numFPrimers = forPrimer.size();
 601                 numRPrimers = revPrimer.size();
 602
 603         }
 604         catch(exception& e) {
 605                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 606                 exit(1);
 607         }
 608 }
 609 //***************************************************************************************************************
 610
 611 int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 612         try {
 613
 614                 string rawSequence = seq.getUnaligned();
 615                 int success = bdiffs + 1;       //guilty until proven innocent
 616
 617                 //can you find the barcode
 618                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 619                         string oligo = it->first;
 620                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 621                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 622                                 break;
 623                         }
 624
 625                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 626                                 group = it->second;
 627                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 628                                 success = 0;
 629                                 break;
 630                         }
 631                 }
 632
 633                 //if you found the barcode or if you don't want to allow for diffs
 634 //              cout << success;
 635                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 636
 637                 else { //try aligning and see if you can find it
 638 //                      cout << endl;
 639
 640                         int maxLength = 0;
 641
 642                         Alignment* alignment;
 643                         if (barcodes.size() > 0) {
 644                                 map<string,int>::iterator it=barcodes.begin();
 645
 646                                 for(it;it!=barcodes.end();it++){
 647                                         if(it->first.length() > maxLength){
 648                                                 maxLength = it->first.length();
 649                                         }
 650                                 }
 651                                 alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+bdiffs+1));
 652
 653                         }else{ alignment = NULL; }
 654
 655                         //can you find the barcode
 656                         int minDiff = 1e6;
 657                         int minCount = 1;
 658                         int minGroup = -1;
 659                         int minPos = 0;
 660
 661                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 662                                 string oligo = it->first;
 663 //                              int length = oligo.length();
 664
 665                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 666                                         success = bdiffs + 10;
 667                                         break;
 668                                 }
 669
 670                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 671                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 672                                 oligo = alignment->getSeqAAln();
 673                                 string temp = alignment->getSeqBAln();
 674
 675                                 int alnLength = oligo.length();
 676
 677                                 for(int i=oligo.length()-1;i>=0;i--){
 678                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 679                                 }
 680                                 oligo = oligo.substr(0,alnLength);
 681                                 temp = temp.substr(0,alnLength);
 682
 683                                 int newStart=0;
 684                                 int numDiff = countDiffs(oligo, temp);
 685                                 if(numDiff < minDiff){
 686                                         minDiff = numDiff;
 687                                         minCount = 1;
 688                                         minGroup = it->second;
 689                                         minPos = 0;
 690                                         for(int i=0;i<alnLength;i++){
 691                                                 if(temp[i] != '-'){
 692                                                         minPos++;
 693                                                 }
 694                                         }
 695                                 }
 696                                 else if(numDiff == minDiff){
 697                                         minCount++;
 698                                 }
 699
 700                         }
 701
 702                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
 703                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
 704                         else{                                                                                                   //use the best match
 705                                 group = minGroup;
 706                                 seq.setUnaligned(rawSequence.substr(minPos));
 707                                 success = minDiff;
 708                         }
 709
 710                         if (alignment != NULL) {  delete alignment;  }
 711
 712                 }
 713 //              cout << success << endl;
 714
 715                 return success;
 716
 717         }
 718         catch(exception& e) {
 719                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
 720                 exit(1);
 721         }
 722
 723 }
 724
 725 //***************************************************************************************************************
 726
 727 int TrimSeqsCommand::stripForward(Sequence& seq){
 728         try {
 729                 string rawSequence = seq.getUnaligned();
 730                 int success = pdiffs + 1;       //guilty until proven innocent
 731
 732                 //can you find the primer
 733                 for(int i=0;i<numFPrimers;i++){
 734                         string oligo = forPrimer[i];
 735
 736                         if(rawSequence.length() < oligo.length()){
 737                                 success = pdiffs + 1;
 738                                 break;
 739                         }
 740
 741                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 742                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 743                                 success = 0;
 744                                 break;
 745                         }
 746                 }
 747
 748                 //if you found the barcode or if you don't want to allow for diffs
 749 //              cout << success;
 750                 if ((pdiffs == 0) || (success == 0)) { return success;  }
 751
 752                 else { //try aligning and see if you can find it
 753 //                      cout << endl;
 754
 755                         int maxLength = 0;
 756
 757                         Alignment* alignment;
 758                         if (numFPrimers > 0) {
 759
 760                                 for(int i=0;i<numFPrimers;i++){
 761                                         if(forPrimer[i].length() > maxLength){
 762                                                 maxLength = forPrimer[i].length();
 763                                         }
 764                                 }
 765                                 alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+pdiffs+1));
 766
 767                         }else{ alignment = NULL; }
 768
 769                         //can you find the barcode
 770                         int minDiff = 1e6;
 771                         int minCount = 1;
 772                         int minPos = 0;
 773
 774                         for(int i=0;i<numFPrimers;i++){
 775                                 string oligo = forPrimer[i];
 776
 777                                 if(rawSequence.length() < maxLength){
 778                                         success = pdiffs + 100;
 779                                         break;
 780                                 }
 781
 782                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 783                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 784                                 oligo = alignment->getSeqAAln();
 785                                 string temp = alignment->getSeqBAln();
 786
 787                                 int alnLength = oligo.length();
 788
 789                                 for(int i=oligo.length()-1;i>=0;i--){
 790                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 791                                 }
 792                                 oligo = oligo.substr(0,alnLength);
 793                                 temp = temp.substr(0,alnLength);
 794
 795                                 int newStart=0;
 796                                 int numDiff = countDiffs(oligo, temp);
 797                                 if(numDiff < minDiff){
 798                                         minDiff = numDiff;
 799                                         minCount = 1;
 800                                         minPos = 0;
 801                                         for(int i=0;i<alnLength;i++){
 802                                                 if(temp[i] != '-'){
 803                                                         minPos++;
 804                                                 }
 805                                         }
 806                                 }
 807                                 else if(numDiff == minDiff){
 808                                         minCount++;
 809                                 }
 810
 811                         }
 812                         if(minDiff > pdiffs)    {       success =  minDiff;             }
 813                         else if(minCount > 1)   {       success =  pdiffs + 10; }
 814                         else{
 815                                 seq.setUnaligned(rawSequence.substr(minPos));
 816                                 success = minDiff;
 817                         }
 818
 819                         if (alignment != NULL) {  delete alignment;  }
 820
 821                 }
 822                 return success;
 823
 824         }
 825         catch(exception& e) {
 826                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
 827                 exit(1);
 828         }
 829 }
 830
 831 //***************************************************************************************************************
 832
 833 bool TrimSeqsCommand::stripReverse(Sequence& seq){
 834         try {
 835                 string rawSequence = seq.getUnaligned();
 836                 bool success = 0;       //guilty until proven innocent
 837
 838                 for(int i=0;i<numRPrimers;i++){
 839                         string oligo = revPrimer[i];
 840
 841                         if(rawSequence.length() < oligo.length()){
 842                                 success = 0;
 843                                 break;
 844                         }
 845
 846                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 847                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 848                                 success = 1;
 849                                 break;
 850                         }
 851                 }
 852                 return success;
 853
 854         }
 855         catch(exception& e) {
 856                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
 857                 exit(1);
 858         }
 859 }
 860
 861 //***************************************************************************************************************
 862
 863 bool TrimSeqsCommand::cullLength(Sequence& seq){
 864         try {
 865
 866                 int length = seq.getNumBases();
 867                 bool success = 0;       //guilty until proven innocent
 868
 869                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
 870                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
 871                 else                                                                                            {       success = 0;    }
 872
 873                 return success;
 874
 875         }
 876         catch(exception& e) {
 877                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
 878                 exit(1);
 879         }
 880
 881 }
 882
 883 //***************************************************************************************************************
 884
 885 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
 886         try {
 887                 int longHomoP = seq.getLongHomoPolymer();
 888                 bool success = 0;       //guilty until proven innocent
 889
 890                 if(longHomoP <= maxHomoP){      success = 1;    }
 891                 else                                    {       success = 0;    }
 892
 893                 return success;
 894         }
 895         catch(exception& e) {
 896                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
 897                 exit(1);
 898         }
 899
 900 }
 901
 902 //***************************************************************************************************************
 903
 904 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
 905         try {
 906                 int numNs = seq.getAmbigBases();
 907                 bool success = 0;       //guilty until proven innocent
 908
 909                 if(numNs <= maxAmbig)   {       success = 1;    }
 910                 else                                    {       success = 0;    }
 911
 912                 return success;
 913         }
 914         catch(exception& e) {
 915                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
 916                 exit(1);
 917         }
 918
 919 }
 920
 921 //***************************************************************************************************************
 922
 923 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 924         try {
 925                 bool success = 1;
 926                 int length = oligo.length();
 927
 928                 for(int i=0;i<length;i++){
 929
 930                         if(oligo[i] != seq[i]){
 931                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 932                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 933                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 934                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 935                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 936                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 937                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 938                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 939                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 940                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 941                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 942                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 943
 944                                 if(success == 0)        {       break;   }
 945                         }
 946                         else{
 947                                 success = 1;
 948                         }
 949                 }
 950
 951                 return success;
 952         }
 953         catch(exception& e) {
 954                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
 955                 exit(1);
 956         }
 957
 958 }
 959 //***************************************************************************************************************
 960
 961 int TrimSeqsCommand::countDiffs(string oligo, string seq){
 962         try {
 963
 964                 int length = oligo.length();
 965                 int countDiffs = 0;
 966
 967                 for(int i=0;i<length;i++){
 968
 969                         if(oligo[i] != seq[i]){
 970                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
 971                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
 972                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
 973                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
 974                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
 975                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
 976                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
 977                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
 978                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 979                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 980                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
 981                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
 982
 983                         }
 984                 }
 985
 986                 return countDiffs;
 987         }
 988         catch(exception& e) {
 989                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
 990                 exit(1);
 991         }
 992
 993 }
 994 //***************************************************************************************************************
 995
 996 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
 997         try {
 998                 string rawSequence = seq.getUnaligned();
 999                 int seqLength;  // = rawSequence.length();
1000                 string name, temp, temp2;
1001
1002                 qFile >> name;
1003
1004                 //get rest of line
1005                 temp = "";
1006                 while (!qFile.eof())    {
1007                         char c = qFile.get();
1008                         if (c == 10 || c == 13){        break;  }
1009                         else { temp += c; }
1010                 }
1011
1012                 int pos = temp.find("length");
1013                 if (pos == temp.npos) { m->mothurOut("Cannot find length in qfile for " + seq.getName()); m->mothurOutEndLine();  seqLength = 0;  }
1014                 else {
1015                         string tempLength = temp.substr(pos);
1016                         istringstream iss (tempLength,istringstream::in);
1017                         iss >> temp;
1018                 }
1019
1020                 splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
1021                 convert(temp, seqLength); //converts string to int
1022
1023                 if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); }  }
1024
1025                 int score;
1026                 int end = seqLength;
1027
1028                 for(int i=0;i<seqLength;i++){
1029                         qFile >> score;
1030
1031                         if(score <= qThreshold){
1032                                 end = i;
1033                                 break;
1034                         }
1035                 }
1036                 for(int i=end+1;i<seqLength;i++){
1037                         qFile >> score;
1038                 }
1039
1040                 seq.setUnaligned(rawSequence.substr(0,end));
1041
1042                 return 1;
1043         }
1044         catch(exception& e) {
1045                 m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1046                 exit(1);
1047         }
1048 }
1049
1050 //***************************************************************************************************************
1051
1052 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1053         try {
1054                 string rawSequence = seq.getUnaligned();
1055                 int seqLength = seq.getNumBases();
1056                 bool success = 0;       //guilty until proven innocent
1057                 string name;
1058
1059                 qFile >> name;
1060                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1061
1062                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1063
1064                 float score;
1065                 float average = 0;
1066
1067                 for(int i=0;i<seqLength;i++){
1068                         qFile >> score;
1069                         average += score;
1070                 }
1071                 average /= seqLength;
1072
1073                 if(average >= qAverage) {       success = 1;    }
1074                 else                                    {       success = 0;    }
1075
1076                 return success;
1077         }
1078         catch(exception& e) {
1079                 m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1080                 exit(1);
1081         }
1082 }
1083
1084 //***************************************************************************************************************