};
vector<int> processIDS; //processid
- vector<linePair*> lines;
+ vector<linePair> lines;
- int driver(linePair*, string, string, string, string);
- int createProcesses(string, string, string, string);
+ int driver(linePair, string, string, string, string, map<string, int>&);
+ int createProcesses(string, string, string, string, map<string, int>&);
int divideInHalf(Sequence, string&, string&);
map<string, int> sortFastaFile(string, string);
map<string, int> sortFastaFile(vector<Sequence>&, map<string, string>&, string newFile);
string getNamesFile(string&);
- int setupChimera(string, map<string, int>&);
- int MPIExecute(string, string, string, string);
+ //int setupChimera(string,);
+ int MPIExecute(string, string, string, string, map<string, int>&);
int deconvoluteResults(SequenceParser*, string, string, string);
map<string, int> priority;
+ int setUpForSelfReference(SequenceParser*&, map<string, string>&, map<string, map<string, int> >&, int);
+ int driverGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
+ int createProcessesGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
+ int MPIExecuteGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
#endif
bool abort, realign, trim, trimera, save;
string fastafile, groupfile, templatefile, outputDir, search, namefile, blastlocation;
int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
float divR;
- Chimera* chimera;
vector<string> outputNames;
vector<string> fastaFileNames;
int count;
int numNoParents;
int threadId;
+ map<string, map<string, int> > fileToPriority;
+ map<string, string> fileGroup;
slayerData(){}
slayerData(string o, string fa, string ac, string f, string te, string se, string bl, bool tri, bool trm, bool re, MothurOut* mout, unsigned long long st, unsigned long long en, int ks, int ma, int mis, int win, int minS, int minC, int miBS, int minSN, int par, int it, int inc, int numw, float div, map<string, int> prior, int tid) {
count = 0;
numNoParents = 0;
}
+ slayerData(string o, string fa, string ac, string te, string se, string bl, bool tri, bool trm, bool re, MothurOut* mout, map<string, map<string, int> >& fPriority, map<string, string>& fileG, int ks, int ma, int mis, int win, int minS, int minC, int miBS, int minSN, int par, int it, int inc, int numw, float div, map<string, int> prior, int tid) {
+ outputFName = o;
+ fasta = fa;
+ accnos = ac;
+ templatefile = te;
+ search = se;
+ blastlocation = bl;
+ trimera = tri;
+ trim = trm;
+ realign = re;
+ m = mout;
+ fileGroup = fileG;
+ fileToPriority = fPriority;
+ ksize = ks;
+ match = ma;
+ mismatch = mis;
+ window = win;
+ minSimilarity = minS;
+ minCoverage = minC;
+ minBS = miBS;
+ minSNP = minSN;
+ parents = par;
+ iters = it;
+ increment = inc;
+ numwanted = numw;
+ divR = div;
+ priority = prior;
+ threadId = tid;
+ count = 0;
+ numNoParents = 0;
+ }
+
};
/**************************************************************************************************/
if((count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine(); }
pDataArray->numNoParents = chimera->getNumNoParents();
+ if (pDataArray->numNoParents == count) { pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }
+
out.close();
out2.close();
if (pDataArray->trim) { out3.close(); }
exit(1);
}
}
+
+/**************************************************************************************************/
+
+static DWORD WINAPI MySlayerGroupThreadFunction(LPVOID lpParam){
+ slayerData* pDataArray;
+ pDataArray = (slayerData*)lpParam;
+
+ try {
+
+ int totalSeqs = 0;
+
+ for (map<string, map<string, int> >::iterator itFile = pDataArray->fileToPriority.begin(); itFile != pDataArray->fileToPriority.end(); itFile++) {
+
+ if (pDataArray->m->control_pressed) { return 0; }
+
+ int start = time(NULL);
+ string thisFastaName = itFile->first;
+ map<string, int> thisPriority = itFile->second;
+ string thisoutputFileName = pDataArray->m->getRootName(pDataArray->m->getSimpleName(thisFastaName)) + pDataArray->fileGroup[thisFastaName] + "slayer.chimera";
+ string thisaccnosFileName = pDataArray->m->getRootName(pDataArray->m->getSimpleName(thisFastaName)) + pDataArray->fileGroup[thisFastaName] + "slayer.accnos";
+ string thistrimFastaFileName = pDataArray->m->getRootName(pDataArray->m->getSimpleName(thisFastaName)) + pDataArray->fileGroup[thisFastaName] + "slayer.fasta";
+
+ pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Checking sequences from group: " + pDataArray->fileGroup[thisFastaName] + "."); pDataArray->m->mothurOutEndLine();
+
+ //int numSeqs = driver(lines[0], thisoutputFileName, thisFastaName, thisaccnosFileName, thistrimFastaFileName, thisPriority);
+ ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ ofstream out;
+ pDataArray->m->openOutputFile(thisoutputFileName, out);
+
+ ofstream out2;
+ pDataArray->m->openOutputFile(thisaccnosFileName, out2);
+
+ ofstream out3;
+ if (pDataArray->trim) { pDataArray->m->openOutputFile(thistrimFastaFileName, out3); }
+
+ ifstream inFASTA;
+ pDataArray->m->openInputFile(thisFastaName, inFASTA);
+
+ Chimera* chimera;
+ chimera = new ChimeraSlayer(thisFastaName, pDataArray->templatefile, pDataArray->trim, thisPriority, pDataArray->search, pDataArray->ksize, pDataArray->match, pDataArray->mismatch, pDataArray->window, pDataArray->divR, pDataArray->minSimilarity, pDataArray->minCoverage, pDataArray->minBS, pDataArray->minSNP, pDataArray->parents, pDataArray->iters, pDataArray->increment, pDataArray->numwanted, pDataArray->realign, pDataArray->blastlocation, pDataArray->threadId);
+ chimera->printHeader(out);
+
+ int numSeqs = 0;
+
+ if (pDataArray->m->control_pressed) { out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera; return 0; }
+
+ if (chimera->getUnaligned()) {
+ pDataArray->m->mothurOut("Your template sequences are different lengths, please correct."); pDataArray->m->mothurOutEndLine();
+ out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close();
+ delete chimera;
+ return 0;
+ }
+ int templateSeqsLength = chimera->getLength();
+
+ bool done = false;
+ while (!done) {
+
+ if (pDataArray->m->control_pressed) { out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera; return 1; }
+
+ Sequence* candidateSeq = new Sequence(inFASTA); pDataArray->m->gobble(inFASTA);
+ string candidateAligned = candidateSeq->getAligned();
+
+ if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
+ if (candidateSeq->getAligned().length() != templateSeqsLength) {
+ pDataArray->m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); pDataArray->m->mothurOutEndLine();
+ }else{
+ //find chimeras
+ chimera->getChimeras(candidateSeq);
+
+ if (pDataArray->m->control_pressed) { out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete candidateSeq; delete chimera; return 1; }
+
+ //if you are not chimeric, then check each half
+ data_results wholeResults = chimera->getResults();
+
+ //determine if we need to split
+ bool isChimeric = false;
+
+ if (wholeResults.flag == "yes") {
+ string chimeraFlag = "no";
+ if( (wholeResults.results[0].bsa >= pDataArray->minBS && wholeResults.results[0].divr_qla_qrb >= pDataArray->divR)
+ ||
+ (wholeResults.results[0].bsb >= pDataArray->minBS && wholeResults.results[0].divr_qlb_qra >= pDataArray->divR) ) { chimeraFlag = "yes"; }
+
+
+ if (chimeraFlag == "yes") {
+ if ((wholeResults.results[0].bsa >= pDataArray->minBS) || (wholeResults.results[0].bsb >= pDataArray->minBS)) { isChimeric = true; }
+ }
+ }
+
+ if ((!isChimeric) && pDataArray->trimera) {
+
+ //split sequence in half by bases
+ string leftQuery, rightQuery;
+ Sequence tempSeq(candidateSeq->getName(), candidateAligned);
+ //divideInHalf(tempSeq, leftQuery, rightQuery);
+ string queryUnAligned = tempSeq.getUnaligned();
+ int numBases = int(queryUnAligned.length() * 0.5);
+
+ string queryAligned = tempSeq.getAligned();
+ leftQuery = tempSeq.getAligned();
+ rightQuery = tempSeq.getAligned();
+
+ int baseCount = 0;
+ int leftSpot = 0;
+ for (int i = 0; i < queryAligned.length(); i++) {
+ //if you are a base
+ if (isalpha(queryAligned[i])) {
+ baseCount++;
+ }
+
+ //if you have half
+ if (baseCount >= numBases) { leftSpot = i; break; } //first half
+ }
+
+ //blank out right side
+ for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; }
+
+ //blank out left side
+ for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; }
+
+ //run chimeraSlayer on each piece
+ Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
+ Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
+
+ //find chimeras
+ chimera->getChimeras(left);
+ data_results leftResults = chimera->getResults();
+
+ chimera->getChimeras(right);
+ data_results rightResults = chimera->getResults();
+
+ //if either piece is chimeric then report
+ Sequence trimmed = chimera->print(out, out2, leftResults, rightResults);
+ if (pDataArray->trim) { trimmed.printSequence(out3); }
+
+ delete left; delete right;
+
+ }else { //already chimeric
+ //print results
+ Sequence trimmed = chimera->print(out, out2);
+ if (pDataArray->trim) { trimmed.printSequence(out3); }
+ }
+
+
+ }
+ numSeqs++;
+ }
+
+ delete candidateSeq;
+
+ if (inFASTA.eof()) { break; }
+
+ //report progress
+ if((numSeqs) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs)); pDataArray->m->mothurOutEndLine(); }
+ }
+ //report progress
+ if((numSeqs) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs)); pDataArray->m->mothurOutEndLine(); }
+
+ pDataArray->numNoParents = chimera->getNumNoParents();
+ if (pDataArray->numNoParents == numSeqs) { pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }
+
+ out.close();
+ out2.close();
+ if (pDataArray->trim) { out3.close(); }
+ inFASTA.close();
+ delete chimera;
+
+
+ ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ //append files
+ pDataArray->m->appendFiles(thisoutputFileName, pDataArray->outputFName); pDataArray->m->mothurRemove(thisoutputFileName);
+ pDataArray->m->appendFiles(thisaccnosFileName, pDataArray->accnos); pDataArray->m->mothurRemove(thisaccnosFileName);
+ if (pDataArray->trim) { pDataArray->m->appendFiles(thistrimFastaFileName, pDataArray->fasta); pDataArray->m->mothurRemove(thistrimFastaFileName); }
+ pDataArray->m->mothurRemove(thisFastaName);
+
+ totalSeqs += numSeqs;
+
+ pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + pDataArray->fileGroup[thisFastaName] + "."); pDataArray->m->mothurOutEndLine();
+ }
+
+ pDataArray->count = totalSeqs;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ChimeraSlayerCommand", "MySlayerGroupThreadFunction");
+ exit(1);
+ }
+}
+
#endif
/**************************************************************************************************/
projects / mothur.git / blobdiff