makecontigscommand.h

   1 #ifndef Mothur_makecontigscommand_h
   2 #define Mothur_makecontigscommand_h
   3
   4 //
   5 //  makecontigscommand.h
   6 //  Mothur
   7 //
   8 //  Created by Sarah Westcott on 5/15/12.
   9 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
  10 //
  11
  12 #include "command.hpp"
  13 #include "sequence.hpp"
  14 #include "qualityscores.h"
  15 #include "alignment.hpp"
  16 #include "gotohoverlap.hpp"
  17 #include "needlemanoverlap.hpp"
  18 #include "blastalign.hpp"
  19 #include "noalign.hpp"
  20 #include "trimoligos.h"
  21
  22 struct fastqRead {
  23         vector<int> scores;
  24         string name;
  25         string sequence;
  26
  27         fastqRead() { name = ""; sequence = ""; scores.clear(); };
  28         fastqRead(string n, string s, vector<int> sc) : name(n), sequence(s), scores(sc) {};
  29         ~fastqRead() {};
  30 };
  31
  32 struct pairFastqRead {
  33         fastqRead forward;
  34     fastqRead reverse;
  35
  36         pairFastqRead() {};
  37         pairFastqRead(fastqRead f, fastqRead r) : forward(f), reverse(r){};
  38         ~pairFastqRead() {};
  39 };
  40 /**************************************************************************************************/
  41
  42 class MakeContigsCommand : public Command {
  43 public:
  44     MakeContigsCommand(string);
  45     MakeContigsCommand();
  46     ~MakeContigsCommand(){}
  47
  48     vector<string> setParameters();
  49     string getCommandName()                     { return "make.contigs";                        }
  50     string getCommandCategory()         { return "Sequence Processing";         }
  51     //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
  52
  53         string getHelpString();
  54     string getOutputPattern(string);
  55     string getCitation() { return "http://www.mothur.org/wiki/Make.contigs"; }
  56     string getDescription()             { return "description"; }
  57
  58     int execute();
  59     void help() { m->mothurOut(getHelpString()); }
  60
  61 private:
  62     bool abort, allFiles, createGroup;
  63     string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, file;
  64         float match, misMatch, gapOpen, gapExtend;
  65         int processors, longestBase, threshold, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs;
  66     vector<string> outputNames;
  67
  68     map<int, oligosPair> barcodes;
  69         map<int, oligosPair> primers;
  70     vector<string>  linker;
  71     vector<string>  spacer;
  72         vector<string> primerNameVector;
  73         vector<string> barcodeNameVector;
  74
  75         map<string, int> groupCounts;
  76     map<string, string> groupMap;
  77
  78     fastqRead readFastq(ifstream&, bool&);
  79     vector< vector< vector<string> > > preProcessData(unsigned long int&);
  80     vector< vector<string> > readFileNames(string);
  81     vector< vector<string> > readFastqFiles(unsigned long int&, string, string);
  82     vector< vector<string> > readFastaFiles(unsigned long int&, string, string);
  83     bool checkReads(fastqRead&, fastqRead&, string, string);
  84     int createProcesses(vector< vector<string> >, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
  85     int driver(vector<string>, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
  86     bool getOligos(vector<vector<string> >&, vector< vector<string> >&, string);
  87     string reverseOligo(string);
  88     vector<pairFastqRead> getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques);
  89 };
  90
  91 /**************************************************************************************************/
  92
  93 /**************************************************************************************************/
  94 //custom data structure for threads to use.
  95 // This is passed by void pointer so it can be any data type
  96 // that can be passed using a single void pointer (LPVOID).
  97 struct contigsData {
  98         string outputFasta;
  99         string outputQual;
 100     string outputScrapFasta;
 101         string outputScrapQual;
 102         string outputMisMatches;
 103         string align;
 104     vector<string> files;
 105     vector<vector<string> > fastaFileNames;
 106     vector<vector<string> > qualFileNames;
 107         MothurOut* m;
 108         float match, misMatch, gapOpen, gapExtend;
 109         int count, threshold, threadID, pdiffs, bdiffs, tdiffs;
 110     bool allFiles, createGroup;
 111     map<string, int> groupCounts;
 112     map<string, string> groupMap;
 113     vector<string> primerNameVector;
 114         vector<string> barcodeNameVector;
 115     map<int, oligosPair> barcodes;
 116         map<int, oligosPair> primers;
 117
 118         contigsData(){}
 119         contigsData(vector<string> f, string of, string oq, string osf, string osq, string om, string al, MothurOut* mout, float ma, float misMa, float gapO, float gapE, int thr, map<int, oligosPair> br, map<int, oligosPair> pr, vector<vector<string> > ffn, vector<vector<string> > qfn, vector<string>bnv, vector<string> pnv, int pdf, int bdf, int tdf, bool cg, bool all, int tid) {
 120         files = f;
 121                 outputFasta = of;
 122         outputQual = oq;
 123         outputMisMatches = om;
 124         m = mout;
 125                 match = ma;
 126                 misMatch = misMa;
 127                 gapOpen = gapO;
 128                 gapExtend = gapE;
 129         threshold = thr;
 130                 align = al;
 131                 count = 0;
 132         outputScrapFasta = osf;
 133         outputScrapQual = osq;
 134         fastaFileNames = ffn;
 135         qualFileNames = qfn;
 136         barcodes = br;
 137         primers = pr;
 138         barcodeNameVector = bnv;
 139         primerNameVector = pnv;
 140         pdiffs = pdf;
 141         bdiffs = bdf;
 142         tdiffs = tdf;
 143         allFiles = all;
 144         createGroup = cg;
 145                 threadID = tid;
 146         }
 147 };
 148
 149 /**************************************************************************************************/
 150 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 151 #else
 152 static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
 153         contigsData* pDataArray;
 154         pDataArray = (contigsData*)lpParam;
 155
 156         try {
 157         int longestBase = 1000;
 158         Alignment* alignment;
 159         if(pDataArray->align == "gotoh")                        {       alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, longestBase);                 }
 160                 else if(pDataArray->align == "needleman")       {       alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, longestBase);                            }
 161
 162         int num = 0;
 163         string thisffastafile = pDataArray->files[0];
 164         string thisfqualfile = pDataArray->files[1];
 165         string thisrfastafile = pDataArray->files[2];
 166         string thisrqualfile = pDataArray->files[3];
 167
 168         if (pDataArray->m->debug) {  pDataArray->m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 169
 170                 if(pDataArray->allFiles){
 171                         for (int i = 0; i < pDataArray->fastaFileNames.size(); i++) { //clears old file
 172                                 for (int j = 0; j < pDataArray->fastaFileNames[i].size(); j++) { //clears old file
 173                                         if (pDataArray->fastaFileNames[i][j] != "") {
 174                                                 ofstream temp;
 175                                                 pDataArray->m->openOutputFile(pDataArray->fastaFileNames[i][j], temp);                  temp.close();
 176                         if (thisfqualfile != "") { pDataArray->m->openOutputFile(pDataArray->qualFileNames[i][j], temp);                        temp.close(); }
 177                                         }
 178                                 }
 179                         }
 180                 }
 181
 182         ifstream inFFasta, inRFasta, inFQual, inRQual;
 183         ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
 184         pDataArray->m->openInputFile(thisffastafile, inFFasta);
 185         pDataArray->m->openInputFile(thisrfastafile, inRFasta);
 186         if (thisfqualfile != "") {
 187             pDataArray->m->openInputFile(thisfqualfile, inFQual);
 188             pDataArray->m->openInputFile(thisrqualfile, inRQual);
 189             pDataArray->m->openOutputFile(pDataArray->outputQual, outQual);
 190             pDataArray->m->openOutputFile(pDataArray->outputScrapQual, outScrapQual);
 191         }
 192         pDataArray->m->openOutputFile(pDataArray->outputFasta, outFasta);
 193         pDataArray->m->openOutputFile(pDataArray->outputMisMatches, outMisMatch);
 194         pDataArray->m->openOutputFile(pDataArray->outputScrapFasta, outScrapFasta);
 195
 196         outMisMatch << "Name\tLength\tMisMatches\n";
 197
 198         TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, 0, 0, pDataArray->primers, pDataArray->barcodes);
 199
 200         while ((!inFFasta.eof()) && (!inRFasta.eof())) {
 201
 202             if (pDataArray->m->control_pressed) { break; }
 203
 204             int success = 1;
 205             string trashCode = "";
 206             int currentSeqsDiffs = 0;
 207
 208             //read seqs and quality info
 209             Sequence fSeq(inFFasta); pDataArray->m->gobble(inFFasta);
 210             Sequence rSeq(inRFasta); pDataArray->m->gobble(inRFasta);
 211             QualityScores* fQual = NULL; QualityScores* rQual = NULL;
 212             if (thisfqualfile != "") {
 213                 fQual = new QualityScores(inFQual); pDataArray->m->gobble(inFQual);
 214                 rQual = new QualityScores(inRQual); pDataArray->m->gobble(inRQual);
 215             }
 216
 217             int barcodeIndex = 0;
 218             int primerIndex = 0;
 219
 220             if(pDataArray->barcodes.size() != 0){
 221                 if (thisfqualfile != "") {
 222                     success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
 223                 }else {
 224                     success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
 225                 }
 226                 if(success > pDataArray->bdiffs)                {       trashCode += 'b';       }
 227                 else{ currentSeqsDiffs += success;  }
 228             }
 229
 230             if(pDataArray->primers.size() != 0){
 231                 if (thisfqualfile != "") {
 232                     success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
 233                 }else {
 234                     success = trimOligos.stripForward(fSeq, rSeq, primerIndex);
 235                 }
 236                 if(success > pDataArray->pdiffs)                {       trashCode += 'f';       }
 237                 else{ currentSeqsDiffs += success;  }
 238             }
 239
 240             if (currentSeqsDiffs > pDataArray->tdiffs)  {       trashCode += 't';   }
 241
 242             //flip the reverse reads
 243             rSeq.reverseComplement();
 244             if (thisfqualfile != "") { rQual->flipQScores(); }
 245
 246             //pairwise align
 247             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 248             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 249             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 250             fSeq.setAligned(alignment->getSeqAAln());
 251             rSeq.setAligned(alignment->getSeqBAln());
 252             int length = fSeq.getAligned().length();
 253
 254             //traverse alignments merging into one contiguous seq
 255             string contig = "";
 256             vector<int> contigScores;
 257             int numMismatches = 0;
 258             string seq1 = fSeq.getAligned();
 259             string seq2 = rSeq.getAligned();
 260             vector<int> scores1, scores2;
 261             if (thisfqualfile != "") {
 262                 scores1 = fQual->getQualityScores();
 263                 scores2 = rQual->getQualityScores();
 264                 delete fQual; delete rQual;
 265             }
 266
 267             int overlapStart = fSeq.getStartPos();
 268             int seq2Start = rSeq.getStartPos();
 269             //bigger of the 2 starting positions is the location of the overlapping start
 270             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
 271                 overlapStart = seq2Start;
 272                 for (int i = 0; i < overlapStart; i++) {
 273                     contig += seq1[i];
 274                     if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
 275                 }
 276             }else { //seq1 starts later so take from 0 to overlapStart from seq2
 277                 for (int i = 0; i < overlapStart; i++) {
 278                     contig += seq2[i];
 279                     if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
 280                 }
 281             }
 282
 283             int seq1End = fSeq.getEndPos();
 284             int seq2End = rSeq.getEndPos();
 285             int overlapEnd = seq1End;
 286             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
 287
 288             for (int i = overlapStart; i < overlapEnd; i++) {
 289                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 290                     contig += seq1[i];
 291                     if (thisfqualfile != "") {
 292                         contigScores.push_back(scores1[ABaseMap[i]]);
 293                         if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
 294                     }
 295                 }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
 296                     if (thisfqualfile != "") {
 297                         if (scores2[BBaseMap[i]] < pDataArray->threshold) { } //
 298                         else {
 299                             contig += seq2[i];
 300                             contigScores.push_back(scores2[BBaseMap[i]]);
 301                         }
 302                     }else { contig += seq2[i]; }
 303                 }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
 304                     if (thisfqualfile != "") {
 305                         if (scores1[ABaseMap[i]] < pDataArray->threshold) { } //
 306                         else {
 307                             contig += seq1[i];
 308                             contigScores.push_back(scores1[ABaseMap[i]]);
 309                         }
 310                     }else { contig += seq1[i]; }
 311                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
 312                     if (thisfqualfile != "") {
 313                         char c = seq1[i];
 314                         contigScores.push_back(scores1[ABaseMap[i]]);
 315                         if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
 316                         contig += c;
 317                         numMismatches++;
 318                     }else { numMismatches++; }
 319                 }else { //should never get here
 320                     pDataArray->m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
 321                 }
 322             }
 323
 324             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
 325                 for (int i = overlapEnd; i < length; i++) {
 326                     contig += seq2[i];
 327                     if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
 328                 }
 329             }else { //seq2 ends before seq1 so take from overlap to length from seq1
 330                 for (int i = overlapEnd; i < length; i++) {
 331                     contig += seq1[i];
 332                     if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
 333                 }
 334
 335             }
 336
 337             if(trashCode.length() == 0){
 338                 bool ignore = false;
 339                 if (pDataArray->createGroup) {
 340                     if(pDataArray->barcodes.size() != 0){
 341                         string thisGroup = pDataArray->barcodeNameVector[barcodeIndex];
 342                         if (pDataArray->primers.size() != 0) {
 343                             if (pDataArray->primerNameVector[primerIndex] != "") {
 344                                 if(thisGroup != "") {
 345                                     thisGroup += "." + pDataArray->primerNameVector[primerIndex];
 346                                 }else {
 347                                     thisGroup = pDataArray->primerNameVector[primerIndex];
 348                                 }
 349                             }
 350                         }
 351
 352                         if (pDataArray->m->debug) { pDataArray->m->mothurOut(", group= " + thisGroup + "\n"); }
 353
 354                         int pos = thisGroup.find("ignore");
 355                         if (pos == string::npos) {
 356                             pDataArray->groupMap[fSeq.getName()] = thisGroup;
 357
 358                             map<string, int>::iterator it = pDataArray->groupCounts.find(thisGroup);
 359                             if (it == pDataArray->groupCounts.end()) {  pDataArray->groupCounts[thisGroup] = 1; }
 360                             else { pDataArray->groupCounts[it->first] ++; }
 361                         }else { ignore = true; }
 362                     }
 363                 }
 364
 365                 if(pDataArray->allFiles && !ignore){
 366                     ofstream output;
 367                     pDataArray->m->openOutputFileAppend(pDataArray->fastaFileNames[barcodeIndex][primerIndex], output);
 368                     output << ">" << fSeq.getName() << endl << contig << endl;
 369                     output.close();
 370
 371                     if (thisfqualfile != "") {
 372                         pDataArray->m->openOutputFileAppend(pDataArray->qualFileNames[barcodeIndex][primerIndex], output);
 373                         output << ">" << fSeq.getName() << endl;
 374                         for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; }
 375                         output << endl;
 376                         output.close();
 377                     }
 378                 }
 379
 380                 //output
 381                 outFasta << ">" << fSeq.getName() << endl << contig << endl;
 382                 if (thisfqualfile != "") {
 383                     outQual << ">" << fSeq.getName() << endl;
 384                     for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
 385                     outQual << endl;
 386                 }
 387                 outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
 388             }else {
 389                 //output
 390                 outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
 391                 if (thisfqualfile != "") {
 392                     outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl;
 393                     for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; }
 394                     outScrapQual << endl;
 395                 }
 396             }
 397             num++;
 398
 399                         //report progress
 400                         if((num) % 1000 == 0){  pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine();             }
 401                 }
 402
 403                 //report progress
 404                 if((num) % 1000 != 0){  pDataArray->m->mothurOut(toString(num)); pDataArray->m->mothurOutEndLine();             }
 405
 406         inFFasta.close();
 407         inRFasta.close();
 408         outFasta.close();
 409         outMisMatch.close();
 410         outScrapFasta.close();
 411         if (thisfqualfile != "") {
 412             inFQual.close();
 413             inRQual.close();
 414             outQual.close();
 415             outScrapQual.close();
 416         }
 417         delete alignment;
 418
 419         if (pDataArray->m->control_pressed) {  pDataArray->m->mothurRemove(pDataArray->outputFasta);  pDataArray->m->mothurRemove(pDataArray->outputMisMatches);  pDataArray->m->mothurRemove(pDataArray->outputScrapFasta);  if (thisfqualfile != "") { pDataArray->m->mothurRemove(pDataArray->outputQual); pDataArray->m->mothurRemove(pDataArray->outputScrapQual); } }
 420
 421         return 0;
 422
 423         }
 424         catch(exception& e) {
 425                 pDataArray->m->errorOut(e, "AlignCommand", "MyContigsThreadFunction");
 426                 exit(1);
 427         }
 428 }
 429 #endif
 430
 431
 432 #endif