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                                         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
 381                                         if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
 382                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 383                                         }
 384
 385                                         if(!success)                    {       trashCode += 'q';                                                               }
 386                                 }
 387
 388                                 if(barcodes.size() != 0){
 389                                         success = stripBarcode(currSeq, group);
 390                                         if(success > bdiffs){   trashCode += 'b';       }
 391                                         else{ currentSeqsDiffs += success;  }
 392                                 }
 393
 394                                 if(numFPrimers != 0){
 395                                         success = stripForward(currSeq);
 396                                         if(success > pdiffs){   trashCode += 'f';       }
 397                                         else{ currentSeqsDiffs += success;  }
 398                                 }
 399
 400                                 if (currentSeqsDiffs > tdiffs) { trashCode += 't';   }
 401
 402                                 if(numRPrimers != 0){
 403                                         success = stripReverse(currSeq);
 404                                         if(!success){   trashCode += 'r';       }
 405                                 }
 406
 407                                 if(minLength > 0 || maxLength > 0){
 408                                         success = cullLength(currSeq);
 409                                         if(!success){   trashCode += 'l'; }
 410                                 }
 411                                 if(maxHomoP > 0){
 412                                         success = cullHomoP(currSeq);
 413                                         if(!success){   trashCode += 'h';       }
 414                                 }
 415                                 if(maxAmbig != -1){
 416                                         success = cullAmbigs(currSeq);
 417                                         if(!success){   trashCode += 'n';       }
 418                                 }
 419
 420                                 if(flip){       currSeq.reverseComplement();    }               // should go last
 421
 422                                 if(trashCode.length() == 0){
 423                                         currSeq.setAligned(currSeq.getUnaligned());
 424                                         currSeq.printSequence(outFASTA);
 425                                         if(barcodes.size() != 0){
 426                                                 outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
 427
 428                                                 if(allFiles){
 429                                                         currSeq.printSequence(*fastaFileNames[group]);
 430                                                 }
 431                                         }
 432                                 }
 433                                 else{
 434                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 435                                         currSeq.setUnaligned(origSeq);
 436                                         currSeq.setAligned(origSeq);
 437                                         currSeq.printSequence(scrapFASTA);
 438                                 }
 439                         }
 440                         gobble(inFASTA);
 441                 }
 442
 443                 inFASTA.close();
 444                 outFASTA.close();
 445                 scrapFASTA.close();
 446                 if (oligoFile != "") {   outGroups.close();   }
 447                 if(qFileName != "")     {       qFile.close();  }
 448
 449                 for(int i=0;i<fastaFileNames.size();i++){
 450                         fastaFileNames[i]->close();
 451                         delete fastaFileNames[i];
 452                 }
 453
 454                 return 0;
 455         }
 456         catch(exception& e) {
 457                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 458                 exit(1);
 459         }
 460 }
 461 /**************************************************************************************************/
 462 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames) {
 463         try {
 464 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 465                 int process = 0;
 466                 int exitCommand = 1;
 467                 processIDS.clear();
 468
 469                 //loop through and create all the processes you want
 470                 while (process != processors) {
 471                         int pid = fork();
 472
 473                         if (pid > 0) {
 474                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 475                                 process++;
 476                         }else if (pid == 0){
 477                                 driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, lines[process], qLines[process]);
 478                                 exit(0);
 479                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 480                 }
 481
 482                 //force parent to wait until all the processes are done
 483                 for (int i=0;i<processors;i++) {
 484                         int temp = processIDS[i];
 485                         wait(&temp);
 486                 }
 487
 488                 return exitCommand;
 489 #endif
 490         }
 491         catch(exception& e) {
 492                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 493                 exit(1);
 494         }
 495 }
 496 /**************************************************************************************************/
 497
 498 int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
 499         try {
 500
 501                 lines.clear();
 502
 503                 vector<long int> positions;
 504
 505                 ifstream inFASTA;
 506                 openInputFile(filename, inFASTA);
 507
 508                 string input;
 509                 while(!inFASTA.eof()){
 510                         input = getline(inFASTA);
 511
 512                         if (input.length() != 0) {
 513                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 514                         }
 515                 }
 516                 inFASTA.close();
 517
 518                 int numFastaSeqs = positions.size();
 519
 520                 FILE * pFile;
 521                 long size;
 522
 523                 //get num bytes in file
 524                 pFile = fopen (filename.c_str(),"rb");
 525                 if (pFile==NULL) perror ("Error opening file");
 526                 else{
 527                         fseek (pFile, 0, SEEK_END);
 528                         size=ftell (pFile);
 529                         fclose (pFile);
 530                 }
 531
 532                 int numSeqsPerProcessor = numFastaSeqs / processors;
 533
 534                 for (int i = 0; i < processors; i++) {
 535
 536                         long int startPos = positions[ i * numSeqsPerProcessor ];
 537                         if(i == processors - 1){
 538                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 539                         }else{
 540                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 541                         }
 542                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 543                 }
 544
 545                 return numFastaSeqs;
 546         }
 547         catch(exception& e) {
 548                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 549                 exit(1);
 550         }
 551 }
 552 //***************************************************************************************************************
 553
 554 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*>& outFASTAVec
 555         try {
 556                 ifstream inOligos;
 557                 openInputFile(oligoFile, inOligos);
 558
 559                 ofstream test;
 560
 561                 string type, oligo, group;
 562                 int index=0;
 563
 564                 while(!inOligos.eof()){
 565                         inOligos >> type;
 566
 567                         if(type[0] == '#'){
 568                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 569                         }
 570                         else{
 571                                 inOligos >> oligo;
 572
 573                                 for(int i=0;i<oligo.length();i++){
 574                                         oligo[i] = toupper(oligo[i]);
 575                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 576                                 }
 577
 578                                 if(type == "forward"){
 579                                         forPrimer.push_back(oligo);
 580                                 }
 581                                 else if(type == "reverse"){
 582                                         Sequence oligoRC("reverse", oligo);
 583                                         oligoRC.reverseComplement();
 584                                         revPrimer.push_back(oligoRC.getUnaligned());
 585                                 }
 586                                 else if(type == "barcode"){
 587                                         inOligos >> group;
 588                                         barcodes[oligo]=index++;
 589                                         groupVector.push_back(group);
 590
 591                                         if(allFiles){
 592                                                 //outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
 593                                                 outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 594                                                 outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 595                                         }
 596                                 }
 597                         }
 598                 }
 599
 600                 inOligos.close();
 601
 602                 numFPrimers = forPrimer.size();
 603                 numRPrimers = revPrimer.size();
 604
 605         }
 606         catch(exception& e) {
 607                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 608                 exit(1);
 609         }
 610 }
 611 //***************************************************************************************************************
 612
 613 int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 614         try {
 615
 616                 string rawSequence = seq.getUnaligned();
 617                 int success = bdiffs + 1;       //guilty until proven innocent
 618
 619                 //can you find the barcode
 620                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 621                         string oligo = it->first;
 622                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 623                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 624                                 break;
 625                         }
 626
 627                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 628                                 group = it->second;
 629                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 630                                 success = 0;
 631                                 break;
 632                         }
 633                 }
 634
 635                 //if you found the barcode or if you don't want to allow for diffs
 636 //              cout << success;
 637                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 638
 639                 else { //try aligning and see if you can find it
 640 //                      cout << endl;
 641
 642                         int maxLength = 0;
 643
 644                         Alignment* alignment;
 645                         if (barcodes.size() > 0) {
 646                                 map<string,int>::iterator it=barcodes.begin();
 647
 648                                 for(it;it!=barcodes.end();it++){
 649                                         if(it->first.length() > maxLength){
 650                                                 maxLength = it->first.length();
 651                                         }
 652                                 }
 653                                 alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+bdiffs+1));
 654
 655                         }else{ alignment = NULL; }
 656
 657                         //can you find the barcode
 658                         int minDiff = 1e6;
 659                         int minCount = 1;
 660                         int minGroup = -1;
 661                         int minPos = 0;
 662
 663                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 664                                 string oligo = it->first;
 665 //                              int length = oligo.length();
 666
 667                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 668                                         success = bdiffs + 10;
 669                                         break;
 670                                 }
 671
 672                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 673                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 674                                 oligo = alignment->getSeqAAln();
 675                                 string temp = alignment->getSeqBAln();
 676
 677                                 int alnLength = oligo.length();
 678
 679                                 for(int i=oligo.length()-1;i>=0;i--){
 680                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 681                                 }
 682                                 oligo = oligo.substr(0,alnLength);
 683                                 temp = temp.substr(0,alnLength);
 684
 685                                 int newStart=0;
 686                                 int numDiff = countDiffs(oligo, temp);
 687                                 if(numDiff < minDiff){
 688                                         minDiff = numDiff;
 689                                         minCount = 1;
 690                                         minGroup = it->second;
 691                                         minPos = 0;
 692                                         for(int i=0;i<alnLength;i++){
 693                                                 if(temp[i] != '-'){
 694                                                         minPos++;
 695                                                 }
 696                                         }
 697                                 }
 698                                 else if(numDiff == minDiff){
 699                                         minCount++;
 700                                 }
 701
 702                         }
 703
 704                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
 705                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
 706                         else{                                                                                                   //use the best match
 707                                 group = minGroup;
 708                                 seq.setUnaligned(rawSequence.substr(minPos));
 709                                 success = minDiff;
 710                         }
 711
 712                         if (alignment != NULL) {  delete alignment;  }
 713
 714                 }
 715 //              cout << success << endl;
 716
 717                 return success;
 718
 719         }
 720         catch(exception& e) {
 721                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
 722                 exit(1);
 723         }
 724
 725 }
 726
 727 //***************************************************************************************************************
 728
 729 int TrimSeqsCommand::stripForward(Sequence& seq){
 730         try {
 731                 string rawSequence = seq.getUnaligned();
 732                 int success = pdiffs + 1;       //guilty until proven innocent
 733
 734                 //can you find the primer
 735                 for(int i=0;i<numFPrimers;i++){
 736                         string oligo = forPrimer[i];
 737
 738                         if(rawSequence.length() < oligo.length()){
 739                                 success = pdiffs + 1;
 740                                 break;
 741                         }
 742
 743                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 744                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 745                                 success = 0;
 746                                 break;
 747                         }
 748                 }
 749
 750                 //if you found the barcode or if you don't want to allow for diffs
 751 //              cout << success;
 752                 if ((pdiffs == 0) || (success == 0)) { return success;  }
 753
 754                 else { //try aligning and see if you can find it
 755 //                      cout << endl;
 756
 757                         int maxLength = 0;
 758
 759                         Alignment* alignment;
 760                         if (numFPrimers > 0) {
 761
 762                                 for(int i=0;i<numFPrimers;i++){
 763                                         if(forPrimer[i].length() > maxLength){
 764                                                 maxLength = forPrimer[i].length();
 765                                         }
 766                                 }
 767                                 alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+pdiffs+1));
 768
 769                         }else{ alignment = NULL; }
 770
 771                         //can you find the barcode
 772                         int minDiff = 1e6;
 773                         int minCount = 1;
 774                         int minPos = 0;
 775
 776                         for(int i=0;i<numFPrimers;i++){
 777                                 string oligo = forPrimer[i];
 778
 779                                 if(rawSequence.length() < maxLength){
 780                                         success = pdiffs + 100;
 781                                         break;
 782                                 }
 783
 784                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 785                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
 786                                 oligo = alignment->getSeqAAln();
 787                                 string temp = alignment->getSeqBAln();
 788
 789                                 int alnLength = oligo.length();
 790
 791                                 for(int i=oligo.length()-1;i>=0;i--){
 792                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 793                                 }
 794                                 oligo = oligo.substr(0,alnLength);
 795                                 temp = temp.substr(0,alnLength);
 796
 797                                 int newStart=0;
 798                                 int numDiff = countDiffs(oligo, temp);
 799                                 if(numDiff < minDiff){
 800                                         minDiff = numDiff;
 801                                         minCount = 1;
 802                                         minPos = 0;
 803                                         for(int i=0;i<alnLength;i++){
 804                                                 if(temp[i] != '-'){
 805                                                         minPos++;
 806                                                 }
 807                                         }
 808                                 }
 809                                 else if(numDiff == minDiff){
 810                                         minCount++;
 811                                 }
 812
 813                         }
 814                         if(minDiff > pdiffs)    {       success =  minDiff;             }
 815                         else if(minCount > 1)   {       success =  pdiffs + 10; }
 816                         else{
 817                                 seq.setUnaligned(rawSequence.substr(minPos));
 818                                 success = minDiff;
 819                         }
 820
 821                         if (alignment != NULL) {  delete alignment;  }
 822
 823                 }
 824                 return success;
 825
 826         }
 827         catch(exception& e) {
 828                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
 829                 exit(1);
 830         }
 831 }
 832
 833 //***************************************************************************************************************
 834
 835 bool TrimSeqsCommand::stripReverse(Sequence& seq){
 836         try {
 837                 string rawSequence = seq.getUnaligned();
 838                 bool success = 0;       //guilty until proven innocent
 839
 840                 for(int i=0;i<numRPrimers;i++){
 841                         string oligo = revPrimer[i];
 842
 843                         if(rawSequence.length() < oligo.length()){
 844                                 success = 0;
 845                                 break;
 846                         }
 847
 848                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
 849                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
 850                                 success = 1;
 851                                 break;
 852                         }
 853                 }
 854                 return success;
 855
 856         }
 857         catch(exception& e) {
 858                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
 859                 exit(1);
 860         }
 861 }
 862
 863 //***************************************************************************************************************
 864
 865 bool TrimSeqsCommand::cullLength(Sequence& seq){
 866         try {
 867
 868                 int length = seq.getNumBases();
 869                 bool success = 0;       //guilty until proven innocent
 870
 871                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
 872                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
 873                 else                                                                                            {       success = 0;    }
 874
 875                 return success;
 876
 877         }
 878         catch(exception& e) {
 879                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
 880                 exit(1);
 881         }
 882
 883 }
 884
 885 //***************************************************************************************************************
 886
 887 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
 888         try {
 889                 int longHomoP = seq.getLongHomoPolymer();
 890                 bool success = 0;       //guilty until proven innocent
 891
 892                 if(longHomoP <= maxHomoP){      success = 1;    }
 893                 else                                    {       success = 0;    }
 894
 895                 return success;
 896         }
 897         catch(exception& e) {
 898                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
 899                 exit(1);
 900         }
 901
 902 }
 903
 904 //***************************************************************************************************************
 905
 906 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
 907         try {
 908                 int numNs = seq.getAmbigBases();
 909                 bool success = 0;       //guilty until proven innocent
 910
 911                 if(numNs <= maxAmbig)   {       success = 1;    }
 912                 else                                    {       success = 0;    }
 913
 914                 return success;
 915         }
 916         catch(exception& e) {
 917                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
 918                 exit(1);
 919         }
 920
 921 }
 922
 923 //***************************************************************************************************************
 924
 925 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
 926         try {
 927                 bool success = 1;
 928                 int length = oligo.length();
 929
 930                 for(int i=0;i<length;i++){
 931
 932                         if(oligo[i] != seq[i]){
 933                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
 934                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
 935                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
 936                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
 937                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
 938                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
 939                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
 940                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
 941                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 942                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
 943                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
 944                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
 945
 946                                 if(success == 0)        {       break;   }
 947                         }
 948                         else{
 949                                 success = 1;
 950                         }
 951                 }
 952
 953                 return success;
 954         }
 955         catch(exception& e) {
 956                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
 957                 exit(1);
 958         }
 959
 960 }
 961 //***************************************************************************************************************
 962
 963 int TrimSeqsCommand::countDiffs(string oligo, string seq){
 964         try {
 965
 966                 int length = oligo.length();
 967                 int countDiffs = 0;
 968
 969                 for(int i=0;i<length;i++){
 970
 971                         if(oligo[i] != seq[i]){
 972                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
 973                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
 974                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
 975                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
 976                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
 977                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
 978                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
 979                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
 980                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 981                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
 982                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
 983                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
 984
 985                         }
 986                 }
 987
 988                 return countDiffs;
 989         }
 990         catch(exception& e) {
 991                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
 992                 exit(1);
 993         }
 994
 995 }
 996 //***************************************************************************************************************
 997
 998 bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
 999         try {
1000 //              string rawSequence = seq.getUnaligned();
1001 //              int seqLength;  // = rawSequence.length();
1002 //              string name, temp, temp2;
1003 //
1004 //              qFile >> name;
1005 //
1006 //              //get rest of line
1007 //              temp = "";
1008 //              while (!qFile.eof())    {
1009 //                      char c = qFile.get();
1010 //                      if (c == 10 || c == 13){        break;  }
1011 //                      else { temp += c; }
1012 //              }
1013 //
1014 //              int pos = temp.find("length");
1015 //              if (pos == temp.npos) { m->mothurOut("Cannot find length in qfile for " + seq.getName()); m->mothurOutEndLine();  seqLength = 0;  }
1016 //              else {
1017 //                      string tempLength = temp.substr(pos);
1018 //                      istringstream iss (tempLength,istringstream::in);
1019 //                      iss >> temp;
1020 //              }
1021 //
1022 //              splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
1023 //              convert(temp, seqLength); //converts string to int
1024 //
1025 //              if (name.length() != 0) {  if(name.substr(1) != seq.getName())  {       m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); }  }
1026
1027                 string rawSequence = seq.getUnaligned();
1028                 int seqLength = seq.getNumBases();
1029                 bool success = 0;       //guilty until proven innocent
1030                 string name;
1031
1032                 qFile >> name;
1033                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1034
1035                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1036
1037                 int score;
1038                 int end = seqLength;
1039
1040                 for(int i=0;i<seqLength;i++){
1041                         qFile >> score;
1042
1043                         if(score < qThreshold){
1044                                 end = i;
1045                                 break;
1046                         }
1047                 }
1048                 for(int i=end+1;i<seqLength;i++){
1049                         qFile >> score;
1050                 }
1051
1052                 seq.setUnaligned(rawSequence.substr(0,end));
1053
1054                 return 1;
1055         }
1056         catch(exception& e) {
1057                 m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1058                 exit(1);
1059         }
1060 }
1061
1062 //***************************************************************************************************************
1063
1064 bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1065         try {
1066                 string rawSequence = seq.getUnaligned();
1067                 int seqLength = seq.getNumBases();
1068                 bool success = 0;       //guilty until proven innocent
1069                 string name;
1070
1071                 qFile >> name;
1072                 if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1073
1074                 while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1075
1076                 float score;
1077                 float average = 0;
1078
1079                 for(int i=0;i<seqLength;i++){
1080                         qFile >> score;
1081                         average += score;
1082                 }
1083                 average /= seqLength;
1084
1085                 if(average >= qAverage) {       success = 1;    }
1086                 else                                    {       success = 0;    }
1087
1088                 return success;
1089         }
1090         catch(exception& e) {
1091                 m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1092                 exit(1);
1093         }
1094 }
1095
1096 //***************************************************************************************************************