#include "mothur.h"
#include "command.hpp"
#include "chimera.h"
+#include "chimeraslayer.h"
/***********************************************************/
vector<int> processIDS; //processid
vector<linePair*> lines;
+ map<string, int> priority;
int driver(linePair*, string, string, string, string);
int createProcesses(string, string, string, string);
/***********************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+typedef struct slayerData {
+ string outputFName;
+ string fasta;
+ string accnos;
+ string filename;
+ string templatefile;
+ string search;
+ string blastlocation;
+ bool trimera;
+ bool trim, realign;
+ unsigned long int start;
+ unsigned long int end;
+ int ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted;
+ MothurOut* m;
+ float divR;
+ map<string, int> priority;
+ int count;
+ int numNoParents;
+ int threadId;
+
+ 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 int st, unsigned long int 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) {
+ outputFName = o;
+ fasta = fa;
+ accnos = ac;
+ filename = f;
+ templatefile = te;
+ search = se;
+ blastlocation = bl;
+ trimera = tri;
+ trim = trm;
+ realign = re;
+ m = mout;
+ start = st;
+ end = en;
+ 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 defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
+ slayerData* pDataArray;
+ pDataArray = (slayerData*)lpParam;
+
+ try {
+ ofstream out;
+ pDataArray->m->openOutputFile(pDataArray->outputFName, out);
+
+ ofstream out2;
+ pDataArray->m->openOutputFile(pDataArray->accnos, out2);
+
+ ofstream out3;
+ if (pDataArray->trim) { pDataArray->m->openOutputFile(pDataArray->fasta, out3); }
+
+ ifstream inFASTA;
+ pDataArray->m->openInputFile(pDataArray->filename, inFASTA);
+
+
+
+ Chimera* chimera;
+ if (pDataArray->templatefile != "self") { //you want to run slayer with a reference template
+ chimera = new ChimeraSlayer(pDataArray->filename, pDataArray->templatefile, pDataArray->trim, 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);
+ }else {
+ chimera = new ChimeraSlayer(pDataArray->filename, pDataArray->templatefile, pDataArray->trim, pDataArray->priority, 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);
+ }
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ chimera->printHeader(out);
+ inFASTA.seekg(0);
+ }else { //this accounts for the difference in line endings.
+ inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA);
+ }
+
+ pDataArray->count = pDataArray->end;
+
+ 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();
+
+ if (pDataArray->start == 0) { chimera->printHeader(out); }
+
+ int count = 0;
+ for(int i = 0; i < pDataArray->end; i++){
+
+ 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) { 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); }
+ }
+
+
+ }
+ count++;
+ }
+
+ delete candidateSeq;
+ //report progress
+ if((count) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine(); }
+ }
+ //report progress
+ if((count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine(); }
+
+ pDataArray->numNoParents = chimera->getNumNoParents();
+ out.close();
+ out2.close();
+ if (pDataArray->trim) { out3.close(); }
+ inFASTA.close();
+ delete chimera;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "ChimeraSlayerCommand", "MySlayerThreadFunction");
+ exit(1);
+ }
+}
+#endif
+
+/**************************************************************************************************/
+
+
#endif
projects / mothur.git / blobdiff