X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=c30404ff965012565b39b8aec0cda823a3bfd139;hb=2bbb7273d4bf5209f098c764551c6e072d60df36;hp=57ed7130916b0e1d810b470fa0552dc5556a1143;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp index 57ed713..c30404f 100644 --- a/chimeraslayer.cpp +++ b/chimeraslayer.cpp @@ -12,21 +12,94 @@ #include "kmerdb.hpp" //*************************************************************************************************************** -ChimeraSlayer::ChimeraSlayer(string mode, bool r, string f) : searchMethod(mode), realign(r), fastafile(f) { - decalc = new DeCalculator(); +ChimeraSlayer::ChimeraSlayer(string file, string temp, string mode, int k, int ms, int mms, int win, float div, +int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() { + try { + fastafile = file; + templateFileName = temp; templateSeqs = readSeqs(temp); + searchMethod = mode; + kmerSize = k; + match = ms; + misMatch = mms; + window = win; + divR = div; + minSim = minsim; + minCov = mincov; + minBS = minbs; + minSNP = minsnp; + parents = par; + iters = it; + increment = inc; + numWanted = numw; + realign = r; + + decalc = new DeCalculator(); + + doPrep(); + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer"); + exit(1); + } } //*************************************************************************************************************** int ChimeraSlayer::doPrep() { try { - + + + //read in all query seqs + vector tempQuerySeqs = readSeqs(fastafile); + + vector temp = templateSeqs; + for (int i = 0; i < tempQuerySeqs.size(); i++) { temp.push_back(tempQuerySeqs[i]); } + + createFilter(temp, 0.0); //just removed columns where all seqs have a gap + + for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; } + + if (m->control_pressed) { return 0; } + + //run filter on template + for (int i = 0; i < templateSeqs.size(); i++) { if (m->control_pressed) { return 0; } runFilter(templateSeqs[i]); } + string kmerDBNameLeft; string kmerDBNameRight; - + //generate the kmerdb to pass to maligner if (searchMethod == "kmer") { - //leftside + string rightTemplateFileName = "right." + templateFileName; + databaseRight = new KmerDB(rightTemplateFileName, kmerSize); + string leftTemplateFileName = "left." + templateFileName; - databaseLeft = new KmerDB(leftTemplateFileName, kmerSize); + databaseLeft = new KmerDB(leftTemplateFileName, kmerSize); + #ifdef USE_MPI + for (int i = 0; i < templateSeqs.size(); i++) { + + if (m->control_pressed) { return 0; } + + string leftFrag = templateSeqs[i]->getUnaligned(); + leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33)); + + Sequence leftTemp(templateSeqs[i]->getName(), leftFrag); + databaseLeft->addSequence(leftTemp); + } + databaseLeft->generateDB(); + databaseLeft->setNumSeqs(templateSeqs.size()); + + for (int i = 0; i < templateSeqs.size(); i++) { + if (m->control_pressed) { return 0; } + + string rightFrag = templateSeqs[i]->getUnaligned(); + rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66)); + + Sequence rightTemp(templateSeqs[i]->getName(), rightFrag); + databaseRight->addSequence(rightTemp); + } + databaseRight->generateDB(); + databaseRight->setNumSeqs(templateSeqs.size()); + + #else + //leftside kmerDBNameLeft = leftTemplateFileName.substr(0,leftTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer"; ifstream kmerFileTestLeft(kmerDBNameLeft.c_str()); @@ -52,8 +125,6 @@ int ChimeraSlayer::doPrep() { databaseLeft->setNumSeqs(templateSeqs.size()); //rightside - string rightTemplateFileName = "right." + templateFileName; - databaseRight = new KmerDB(rightTemplateFileName, kmerSize); kmerDBNameRight = rightTemplateFileName.substr(0,rightTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer"; ifstream kmerFileTestRight(kmerDBNameRight.c_str()); @@ -76,40 +147,8 @@ int ChimeraSlayer::doPrep() { kmerFileTestRight.close(); databaseRight->setNumSeqs(templateSeqs.size()); - - } - - int start = time(NULL); - //filter the sequences - //read in all query seqs - ifstream in; - openInputFile(fastafile, in); - - vector tempQuerySeqs; - while(!in.eof()){ - if (m->control_pressed) { for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; } return 0; } - - Sequence* s = new Sequence(in); - gobble(in); - - if (s->getName() != "") { tempQuerySeqs.push_back(s); } + #endif } - in.close(); - - vector temp = templateSeqs; - for (int i = 0; i < tempQuerySeqs.size(); i++) { temp.push_back(tempQuerySeqs[i]); } - - createFilter(temp, 0.0); //just removed columns where all seqs have a gap - - for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; } - - if (m->control_pressed) { return 0; } - - - //run filter on template - for (int i = 0; i < templateSeqs.size(); i++) { if (m->control_pressed) { return 0; } runFilter(templateSeqs[i]); } - - m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to filter."); m->mothurOutEndLine(); return 0; @@ -158,13 +197,67 @@ int ChimeraSlayer::print(ostream& out, ostream& outAcc) { exit(1); } } +#ifdef USE_MPI +//*************************************************************************************************************** +int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { + try { + MPI_Status status; + bool results = false; + string outAccString = ""; + string outputString = ""; + + if (chimeraFlags == "yes") { + string chimeraFlag = "no"; + if( (chimeraResults[0].bsa >= minBS && chimeraResults[0].divr_qla_qrb >= divR) + || + (chimeraResults[0].bsb >= minBS && chimeraResults[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; } + + + if (chimeraFlag == "yes") { + if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) { + cout << querySeq->getName() << "\tyes" << endl; + outAccString += querySeq->getName() + "\n"; + results = true; + + //write to accnos file + int length = outAccString.length(); + char* buf2 = new char[length]; + memcpy(buf2, outAccString.c_str(), length); + + MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status); + delete buf2; + } + } + + outputString = getBlock(chimeraResults[0]); + outputString += "\n"; + + }else { outputString += querySeq->getName() + "\tno\n"; } + + //write to output file + int length = outputString.length(); + char* buf = new char[length]; + memcpy(buf, outputString.c_str(), length); + + MPI_File_write_shared(out, buf, length, MPI_CHAR, &status); + delete buf; + + return results; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "print"); + exit(1); + } +} +#endif + //*************************************************************************************************************** int ChimeraSlayer::getChimeras(Sequence* query) { try { chimeraFlags = "no"; //filter query - spotMap = runFilter(query); + spotMap = runFilter(query); querySeq = query; @@ -274,7 +367,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) { //*************************************************************************************************************** void ChimeraSlayer::printBlock(data_struct data, ostream& out){ try { - //out << "Name\tParentA\tParentB\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n"; + //out << ":)\n"; out << querySeq->getName() << '\t'; out << data.parentA.getName() << "\t" << data.parentB.getName() << '\t'; @@ -307,4 +400,25 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){ } } //*************************************************************************************************************** +string ChimeraSlayer::getBlock(data_struct data){ + try { + + string outputString = ""; + + outputString += querySeq->getName() + "\t"; + outputString += data.parentA.getName() + "\t" + data.parentB.getName() + "\t"; + + outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t"; + outputString += toString(data.divr_qlb_qra) + "\t" + toString(data.qlb_qra) + "\t" + toString(data.bsb) + "\t"; + + outputString += "yes\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t"; + + return outputString; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "getBlock"); + exit(1); + } +} +//***************************************************************************************************************/