trimseqscommand.cpp

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