aligncommand.cpp

   1 /*
   2  *  aligncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/15/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  *      This version of nast does everything I think that the greengenes nast server does and then some.  I have added the
   9  *      feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
  10  *      method.  This latter feature is perhaps most significant.  nastPlus enables a user to use either a Needleman-Wunsch
  11  *      (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm.  This is significant because it
  12  *      allows for a global alignment and not the local alignment provided by bLAst.  Furthermore, it has the potential to
  13  *      provide a better alignment because of the banding method employed by blast (I'm not sure about this).
  14  *
  15  */
  16
  17 #include "aligncommand.h"
  18 #include "sequence.hpp"
  19
  20 #include "gotohoverlap.hpp"
  21 #include "needlemanoverlap.hpp"
  22 #include "blastalign.hpp"
  23 #include "noalign.hpp"
  24
  25 #include "nast.hpp"
  26 #include "nastreport.hpp"
  27
  28
  29 //**********************************************************************************************************************
  30
  31 AlignCommand::AlignCommand(string option){
  32         try {
  33                 //              globaldata = GlobalData::getInstance();
  34                 abort = false;
  35
  36                 //allow user to run help
  37                 if(option == "help") { help(); abort = true; }
  38
  39                 else {
  40
  41                         //valid paramters for this command
  42                         string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold"};
  43                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  44
  45                         OptionParser parser(option);
  46                         map<string, string> parameters = parser.getParameters();
  47
  48                         ValidParameters validParameter;
  49
  50                         //check to make sure all parameters are valid for command
  51                         for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  52                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  53                         }
  54
  55                         //check for required parameters
  56                         templateFileName = validParameter.validFile(parameters, "template", true);
  57                         if (templateFileName == "not found") {
  58                                 mothurOut("template is a required parameter for the align.seqs command.");
  59                                 mothurOutEndLine();
  60                                 abort = true;
  61                         }
  62                         else if (templateFileName == "not open") { abort = true; }
  63
  64                         candidateFileName = validParameter.validFile(parameters, "candidate", false);
  65                         if (candidateFileName == "not found") { mothurOut("candidate is a required parameter for the align.seqs command."); mothurOutEndLine(); abort = true;  }
  66                         else {
  67                                 splitAtDash(candidateFileName, candidateFileNames);
  68
  69                                 //go through files and make sure they are good, if not, then disregard them
  70                                 for (int i = 0; i < candidateFileNames.size(); i++) {
  71                                         int ableToOpen;
  72                                         ifstream in;
  73                                         ableToOpen = openInputFile(candidateFileNames[i], in);
  74                                         if (ableToOpen == 1) {
  75                                                 mothurOut(candidateFileNames[i] + " will be disregarded."); mothurOutEndLine();
  76                                                 //erase from file list
  77                                                 candidateFileNames.erase(candidateFileNames.begin()+i);
  78                                                 i--;
  79                                         }
  80                                         in.close();
  81                                 }
  82
  83                                 //make sure there is at least one valid file left
  84                                 if (candidateFileNames.size() == 0) { mothurOut("no valid files."); mothurOutEndLine(); abort = true; }
  85                         }
  86
  87
  88                         //check for optional parameter and set defaults
  89                         // ...at some point should added some additional type checking...
  90                         string temp;
  91                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
  92                         convert(temp, kmerSize);
  93
  94                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
  95                         convert(temp, match);
  96
  97                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
  98                         convert(temp, misMatch);
  99
 100                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 101                         convert(temp, gapOpen);
 102
 103                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 104                         convert(temp, gapExtend);
 105
 106                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 107                         convert(temp, processors);
 108
 109                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 110                         flip = isTrue(temp);
 111
 112                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 113                         convert(temp, threshold);
 114
 115                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 116
 117                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 118                 }
 119
 120         }
 121         catch(exception& e) {
 122                 errorOut(e, "AlignCommand", "AlignCommand");
 123                 exit(1);
 124         }
 125 }
 126
 127 //**********************************************************************************************************************
 128
 129 AlignCommand::~AlignCommand(){
 130
 131         if (abort == false) {
 132                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 133                 delete templateDB;
 134                 delete alignment;
 135         }
 136 }
 137
 138 //**********************************************************************************************************************
 139
 140 void AlignCommand::help(){
 141         try {
 142                 mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
 143                 mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
 144                 mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
 145                 mothurOut("The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer.\n");
 146                 mothurOut("The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
 147                 mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 148                 mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 149                 mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 150                 mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 151                 mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 152                 mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse compement if a sequence falls below the threshold.  The default is false.\n");
 153                 mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. \n");
 154                 mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
 155                 mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");
 156                 mothurOut("The align.seqs command should be in the following format: \n");
 157                 mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
 158                 mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
 159                 mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
 160         }
 161         catch(exception& e) {
 162                 errorOut(e, "AlignCommand", "help");
 163                 exit(1);
 164         }
 165 }
 166
 167
 168 //**********************************************************************************************************************
 169
 170 int AlignCommand::execute(){
 171         try {
 172                 if (abort == true) {    return 0;       }
 173
 174                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 175                 int longestBase = templateDB->getLongestBase();
 176
 177                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 178                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 179                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 180                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 181                 else {
 182                         mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 183                         mothurOutEndLine();
 184                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 185                 }
 186
 187                 for (int s = 0; s < candidateFileNames.size(); s++) {
 188                         mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); mothurOutEndLine();
 189
 190                         string alignFileName = candidateFileNames[s].substr(0,candidateFileNames[s].find_last_of(".")+1) + "align";
 191                         string reportFileName = candidateFileNames[s].substr(0,candidateFileNames[s].find_last_of(".")+1) + "align.report";
 192                         string accnosFileName = candidateFileNames[s].substr(0,candidateFileNames[s].find_last_of(".")+1) + "flip.accnos";
 193
 194                         int numFastaSeqs = 0;
 195                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 196                         int start = time(NULL);
 197
 198 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 199                         if(processors == 1){
 200                                 ifstream inFASTA;
 201                                 openInputFile(candidateFileNames[s], inFASTA);
 202                                 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 203                                 inFASTA.close();
 204
 205                                 lines.push_back(new linePair(0, numFastaSeqs));
 206
 207                                 driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 208
 209                                 //delete accnos file if its blank else report to user
 210                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  }
 211                                 else {
 212                                         mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 213                                         if (!flip) {
 214                                                 mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 215                                         }else{  mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 216                                         mothurOutEndLine();
 217                                 }
 218                         }
 219                         else{
 220                                 vector<int> positions;
 221                                 processIDS.resize(0);
 222
 223                                 ifstream inFASTA;
 224                                 openInputFile(candidateFileNames[s], inFASTA);
 225
 226                                 string input;
 227                                 while(!inFASTA.eof()){
 228                                         input = getline(inFASTA);
 229                                         if (input.length() != 0) {
 230                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 231                                         }
 232                                 }
 233                                 inFASTA.close();
 234
 235                                 numFastaSeqs = positions.size();
 236
 237                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 238
 239                                 for (int i = 0; i < processors; i++) {
 240                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 241                                         if(i == processors - 1){
 242                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 243                                         }
 244                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 245                                 }
 246
 247                                 createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 248
 249                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 250                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
 251
 252                                 //append alignment and report files
 253                                 for(int i=1;i<processors;i++){
 254                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 255                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 256
 257                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 258                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 259                                 }
 260
 261                                 vector<string> nonBlankAccnosFiles;
 262                                 //delete blank accnos files generated with multiple processes
 263                                 for(int i=0;i<processors;i++){
 264                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 265                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 266                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 267                                 }
 268
 269                                 //append accnos files
 270                                 if (nonBlankAccnosFiles.size() != 0) {
 271                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 272
 273                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 274                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
 275                                                 remove(nonBlankAccnosFiles[h].c_str());
 276                                         }
 277                                         mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 278                                         if (!flip) {
 279                                                 mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 280                                         }else{  mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 281                                         mothurOutEndLine();
 282                                 }
 283                         }
 284 #else
 285                         ifstream inFASTA;
 286                         openInputFile(candidateFileName[s], inFASTA);
 287                         numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 288                         inFASTA.close();
 289
 290                         lines.push_back(new linePair(0, numFastaSeqs));
 291
 292                         driver(lines[0], alignFileName, reportFileName, accnosFileName);
 293
 294                         //delete accnos file if its blank else report to user
 295                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  }
 296                         else {
 297                                 mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 298                                 if (!flip) {
 299                                         mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 300                                 }else{  mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 301                                 mothurOutEndLine();
 302                         }
 303
 304 #endif
 305
 306
 307
 308                         mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 309                         mothurOutEndLine();
 310                         mothurOutEndLine();
 311                 }
 312
 313                 return 0;
 314         }
 315         catch(exception& e) {
 316                 errorOut(e, "AlignCommand", "execute");
 317                 exit(1);
 318         }
 319 }
 320
 321 //**********************************************************************************************************************
 322
 323 int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
 324         try {
 325                 ofstream alignmentFile;
 326                 openOutputFile(alignFName, alignmentFile);
 327
 328                 ofstream accnosFile;
 329                 openOutputFile(accnosFName, accnosFile);
 330
 331                 NastReport report(reportFName);
 332
 333                 ifstream inFASTA;
 334                 openInputFile(filename, inFASTA);
 335
 336                 inFASTA.seekg(line->start);
 337
 338                 for(int i=0;i<line->numSeqs;i++){
 339
 340                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 341                         int origNumBases = candidateSeq->getNumBases();
 342                         string originalUnaligned = candidateSeq->getUnaligned();
 343                         int numBasesNeeded = origNumBases * threshold;
 344
 345                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 346                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 347                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 348                                 }
 349
 350                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 351                                 Sequence* templateSeq = &temp;
 352
 353                                 float searchScore = templateDB->getSearchScore();
 354
 355                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 356                                 Sequence* copy;
 357
 358                                 Nast* nast2;
 359                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 360                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 361                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 362                                                                                                 //so this bool tells you if you need to delete it
 363
 364                                 //if there is a possibility that this sequence should be reversed
 365                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 366
 367                                         string wasBetter = "";
 368                                         //if the user wants you to try the reverse
 369                                         if (flip) {
 370                                                 //get reverse compliment
 371                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 372                                                 copy->reverseComplement();
 373
 374                                                 //rerun alignment
 375                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 376                                                 Sequence* templateSeq2 = &temp2;
 377
 378                                                 searchScore = templateDB->getSearchScore();
 379
 380                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 381
 382                                                 //check if any better
 383                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 384                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 385                                                         templateSeq = templateSeq2;
 386                                                         delete nast;
 387                                                         nast = nast2;
 388                                                         needToDeleteCopy = true;
 389                                                 }else{
 390                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 391                                                         delete nast2;
 392                                                         delete copy;
 393                                                 }
 394                                         }
 395
 396                                         //create accnos file with names
 397                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 398                                 }
 399
 400                                 report.setCandidate(candidateSeq);
 401                                 report.setTemplate(templateSeq);
 402                                 report.setSearchParameters(search, searchScore);
 403                                 report.setAlignmentParameters(align, alignment);
 404                                 report.setNastParameters(*nast);
 405
 406                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 407
 408                                 report.print();
 409                                 delete nast;
 410                                 if (needToDeleteCopy) {   delete copy;   }
 411                         }
 412                         delete candidateSeq;
 413
 414                         //report progress
 415                         if((i+1) % 100 == 0){   mothurOut(toString(i+1)); mothurOutEndLine();           }
 416                 }
 417                 //report progress
 418                 if((line->numSeqs) % 100 != 0){ mothurOut(toString(line->numSeqs)); mothurOutEndLine();         }
 419
 420                 alignmentFile.close();
 421                 inFASTA.close();
 422                 accnosFile.close();
 423
 424                 return 1;
 425         }
 426         catch(exception& e) {
 427                 errorOut(e, "AlignCommand", "driver");
 428                 exit(1);
 429         }
 430 }
 431
 432 /**************************************************************************************************/
 433
 434 void AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 435         try {
 436 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 437                 int process = 0;
 438                 //              processIDS.resize(0);
 439
 440                 //loop through and create all the processes you want
 441                 while (process != processors) {
 442                         int pid = fork();
 443
 444                         if (pid > 0) {
 445                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 446                                 process++;
 447                         }else if (pid == 0){
 448                                 driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 449                                 exit(0);
 450                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 451                 }
 452
 453                 //force parent to wait until all the processes are done
 454                 for (int i=0;i<processors;i++) {
 455                         int temp = processIDS[i];
 456                         wait(&temp);
 457                 }
 458 #endif
 459         }
 460         catch(exception& e) {
 461                 errorOut(e, "AlignCommand", "createProcesses");
 462                 exit(1);
 463         }
 464 }
 465
 466 /**************************************************************************************************/
 467
 468 void AlignCommand::appendAlignFiles(string temp, string filename) {
 469         try{
 470
 471                 ofstream output;
 472                 ifstream input;
 473                 openOutputFileAppend(filename, output);
 474                 openInputFile(temp, input);
 475
 476                 while(char c = input.get()){
 477                         if(input.eof())         {       break;                  }
 478                         else                            {       output << c;    }
 479                 }
 480
 481                 input.close();
 482                 output.close();
 483         }
 484         catch(exception& e) {
 485                 errorOut(e, "AlignCommand", "appendAlignFiles");
 486                 exit(1);
 487         }
 488 }
 489 //**********************************************************************************************************************
 490
 491 void AlignCommand::appendReportFiles(string temp, string filename) {
 492         try{
 493
 494                 ofstream output;
 495                 ifstream input;
 496                 openOutputFileAppend(filename, output);
 497                 openInputFile(temp, input);
 498
 499                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 500
 501                 while(char c = input.get()){
 502                         if(input.eof())         {       break;                  }
 503                         else                            {       output << c;    }
 504                 }
 505
 506                 input.close();
 507                 output.close();
 508         }
 509         catch(exception& e) {
 510                 errorOut(e, "AlignCommand", "appendReportFiles");
 511                 exit(1);
 512         }
 513 }
 514
 515 //**********************************************************************************************************************