*/
#include "chimeraslayer.h"
+#include "chimerarealigner.h"
+#include "kmerdb.hpp"
+#include "blastdb.hpp"
//***************************************************************************************************************
-ChimeraSlayer::ChimeraSlayer(string filename, string temp) { fastafile = filename; templateFile = temp; }
+ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, 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;
+ trimChimera = trim;
+
+ decalc = new DeCalculator();
+
+ doPrep();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-
-ChimeraSlayer::~ChimeraSlayer() {
+ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string name, string mode, string abunds, 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 {
- for (int i = 0; i < querySeqs.size(); i++) { delete querySeqs[i]; }
- for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; }
+ fastafile = file; templateSeqs = readSeqs(fastafile);
+ templateFileName = 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;
+ includeAbunds = abunds;
+ trimChimera = trim;
+
+ //read name file and create nameMapRank
+ readNameFile(name);
+
+ decalc = new DeCalculator();
+
+ createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+
+ //run filter on template
+ for (int i = 0; i < templateSeqs.size(); i++) { runFilter(templateSeqs[i]); }
+
}
catch(exception& e) {
- errorOut(e, "ChimeraSlayer", "~ChimeraSlayer");
+ m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
exit(1);
}
-}
+}
//***************************************************************************************************************
-void ChimeraSlayer::print(ostream& out) {
+int ChimeraSlayer::readNameFile(string name) {
try {
- mothurOutEndLine();
- mothurOut("Only reporting sequence supported by 90% of bootstrapped results.");
- mothurOutEndLine();
-
- for (int i = 0; i < querySeqs.size(); i++) {
-
- if (chimeraFlags[i] == "yes") {
- cout << i << endl;
- if ((chimeraResults[i][0].bsa >= 90.0) || (chimeraResults[i][0].bsb >= 90.0)) {
- mothurOut(querySeqs[i]->getName() + "\tyes"); mothurOutEndLine();
- out << querySeqs[i]->getName() << "\tyes" << endl;
- }else {
- out << querySeqs[i]->getName() << "\tyes" << endl;
- //mothurOut(querySeqs[i]->getName() + "\tno"); mothurOutEndLine();
- }
-
- printBlock(chimeraResults[i][0], out, i);
+ ifstream in;
+ m->openInputFile(name, in);
+
+ int maxRank = 0;
+ int minRank = 10000000;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ string thisname, repnames;
+
+ in >> thisname; m->gobble(in); //read from first column
+ in >> repnames; //read from second column
+
+ map<string, vector<string> >::iterator it = nameMapRank.find(thisname);
+ if (it == nameMapRank.end()) {
- out << endl;
- }else{
- out << querySeqs[i]->getName() << "\tno" << endl;
- //mothurOut(querySeqs[i]->getName() + "\tno"); mothurOutEndLine();
- }
- }
+ vector<string> splitRepNames;
+ m->splitAtComma(repnames, splitRepNames);
+
+ nameMapRank[thisname] = splitRepNames;
+ if (splitRepNames.size() > maxRank) { maxRank = splitRepNames.size(); }
+ if (splitRepNames.size() < minRank) { minRank = splitRepNames.size(); }
+
+ }else{ m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); }
+
+ m->gobble(in);
+ }
+ in.close();
+
+ //sanity check to make sure files match
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ map<string, vector<string> >::iterator it = nameMapRank.find(templateSeqs[i]->getName());
+
+ if (it == nameMapRank.end()) { m->mothurOut("[ERROR]: " + templateSeqs[i]->getName() + " is not in namesfile, but is in fastafile. Every name in fasta file must be in first column of names file."); m->mothurOutEndLine(); m->control_pressed = true; }
+ }
+
+ if (maxRank == minRank) { m->mothurOut("[ERROR]: all sequences in namesfile have the same abundance, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return 0;
+
}
catch(exception& e) {
- errorOut(e, "ChimeraSlayer", "print");
+ m->errorOut(e, "ChimeraSlayer", "readNameFile");
exit(1);
}
}
//***************************************************************************************************************
-int ChimeraSlayer::getChimeras() {
+int ChimeraSlayer::doPrep() {
try {
- //read in query sequences and subject sequences
- mothurOut("Reading sequences and template file... "); cout.flush();
- querySeqs = readSeqs(fastafile);
- templateSeqs = readSeqs(templateFile);
- mothurOut("Done."); mothurOutEndLine();
+ //read in all query seqs
+ vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
+
+ vector<Sequence*> temp = templateSeqs;
+ for (int i = 0; i < tempQuerySeqs.size(); i++) { temp.push_back(tempQuerySeqs[i]); }
- int numSeqs = querySeqs.size();
+ createFilter(temp, 0.0); //just removed columns where all seqs have a gap
- if (unaligned) { mothurOut("Your sequences need to be aligned when you use the chimeraslayer method."); mothurOutEndLine(); return 1; }
+ for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; }
- chimeraResults.resize(numSeqs);
- chimeraFlags.resize(numSeqs, "no");
- spotMap.resize(numSeqs);
+ if (m->control_pressed) { return 0; }
- //break up file if needed
- int linesPerProcess = numSeqs / processors ;
+ //run filter on template
+ for (int i = 0; i < templateSeqs.size(); i++) { if (m->control_pressed) { return 0; } runFilter(templateSeqs[i]); }
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- //find breakup of sequences for all times we will Parallelize
- if (processors == 1) { lines.push_back(new linePair(0, numSeqs)); }
- else {
- //fill line pairs
- for (int i = 0; i < (processors-1); i++) {
- lines.push_back(new linePair((i*linesPerProcess), ((i*linesPerProcess) + linesPerProcess)));
+ string kmerDBNameLeft;
+ string kmerDBNameRight;
+
+ //generate the kmerdb to pass to maligner
+ if (searchMethod == "kmer") {
+ string templatePath = m->hasPath(templateFileName);
+ string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
+ databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
+
+ string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
+ 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());
+ bool needToGenerateLeft = true;
+
+ if(kmerFileTestLeft){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
+ if (GoodFile) { needToGenerateLeft = false; }
+ }
+
+ if(needToGenerateLeft){
+
+ 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();
+
+ }else {
+ databaseLeft->readKmerDB(kmerFileTestLeft);
+ }
+ kmerFileTestLeft.close();
+
+ databaseLeft->setNumSeqs(templateSeqs.size());
+
+ //rightside
+ kmerDBNameRight = rightTemplateFileName.substr(0,rightTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+ ifstream kmerFileTestRight(kmerDBNameRight.c_str());
+ bool needToGenerateRight = true;
+
+ if(kmerFileTestRight){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
+ if (GoodFile) { needToGenerateRight = false; }
+ }
+
+ if(needToGenerateRight){
+
+ 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);
}
- //this is necessary to get remainder of processors / numSeqs so you don't miss any lines at the end
- int i = processors - 1;
- lines.push_back(new linePair((i*linesPerProcess), numSeqs));
+ databaseRight->generateDB();
+
+ }else {
+ databaseRight->readKmerDB(kmerFileTestRight);
}
- #else
- lines.push_back(new linePair(0, numSeqs));
- #endif
+ kmerFileTestRight.close();
+
+ databaseRight->setNumSeqs(templateSeqs.size());
+ #endif
+ }else if (searchMethod == "blast") {
- if (seqMask != "") { decalc = new DeCalculator(); } //to use below
+ //generate blastdb
+ databaseLeft = new BlastDB(-1.0, -1.0, 1, -3);
+
+ for (int i = 0; i < templateSeqs.size(); i++) { databaseLeft->addSequence(*templateSeqs[i]); }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(templateSeqs.size());
+ }
- //initialize spotMap
- for (int j = 0; j < numSeqs; j++) {
- for (int i = 0; i < querySeqs[0]->getAligned().length(); i++) {
- spotMap[j][i] = i;
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "doprep");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<Sequence*> ChimeraSlayer::getTemplate(Sequence* q) {
+ try {
+
+ vector<Sequence*> thisTemplate;
+
+ int thisRank;
+ string thisName = q->getName();
+ map<string, vector<string> >::iterator itRank = nameMapRank.find(thisName); // you will find it because we already sanity checked
+ thisRank = (itRank->second).size();
+
+ //create list of names we want to put into the template
+ set<string> namesToAdd;
+ for (itRank = nameMapRank.begin(); itRank != nameMapRank.end(); itRank++) {
+ if (itRank->first != thisName) {
+ if (includeAbunds == "greaterequal") {
+ if ((itRank->second).size() >= thisRank) {
+ //you are more abundant than me or equal to my abundance
+ for (int i = 0; i < (itRank->second).size(); i++) {
+ namesToAdd.insert((itRank->second)[i]);
+ }
+ }
+ }else if (includeAbunds == "greater") {
+ if ((itRank->second).size() > thisRank) {
+ //you are more abundant than me
+ for (int i = 0; i < (itRank->second).size(); i++) {
+ namesToAdd.insert((itRank->second)[i]);
+ }
+ }
+ }else if (includeAbunds == "all") {
+ //add everyone
+ for (int i = 0; i < (itRank->second).size(); i++) {
+ namesToAdd.insert((itRank->second)[i]);
+ }
+ }
}
}
- //referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity
- maligner = new Maligner(templateSeqs, numWanted, match, misMatch, 1.01, minSim);
- slayer = new Slayer(window, increment, minSim, divR, iters);
-
- for (int i = 0; i < querySeqs.size(); i++) {
-
- string chimeraFlag = maligner->getResults(querySeqs[i]);
- //float percentIdentical = maligner->getPercentID();
- vector<results> Results = maligner->getOutput();
-
- cout << "Processing sequence: " << i+1 << endl;
-
- //for (int j = 0; j < Results.size(); j++) {
- //cout << "regionStart = " << Results[j].regionStart << "\tRegionEnd = " << Results[j].regionEnd << "\tName = " << Results[j].parent << "\tPerQP = " << Results[j].queryToParent << "\tLocalPerQP = " << Results[j].queryToParentLocal << "\tdivR = " << Results[j].divR << endl;
- //}
-
- //if (chimeraFlag == "yes") {
-
- //get sequence that were given from maligner results
- vector<SeqDist> seqs;
- map<string, float> removeDups;
- map<string, float>::iterator itDup;
- for (int j = 0; j < Results.size(); j++) {
- float dist = (Results[j].regionEnd - Results[j].regionStart + 1) * Results[j].queryToParentLocal;
- //only add if you are not a duplicate
- itDup = removeDups.find(Results[j].parent);
- if (itDup == removeDups.end()) { //this is not duplicate
- removeDups[Results[j].parent] = dist;
- }else if (dist > itDup->second) { //is this a stronger number for this parent
- removeDups[Results[j].parent] = dist;
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ if (namesToAdd.count(templateSeqs[i]->getName()) != 0) {
+ thisTemplate.push_back(templateSeqs[i]);
+ }
+ }
+
+ string kmerDBNameLeft;
+ string kmerDBNameRight;
+
+ //generate the kmerdb to pass to maligner
+ if (searchMethod == "kmer") {
+ string templatePath = m->hasPath(templateFileName);
+ string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
+ databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
+
+ string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
+ databaseLeft = new KmerDB(leftTemplateFileName, kmerSize);
+#ifdef USE_MPI
+ for (int i = 0; i < thisTemplate.size(); i++) {
+
+ if (m->control_pressed) { return thisTemplate; }
+
+ string leftFrag = thisTemplate[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(thisTemplate[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(thisTemplate.size());
+
+ for (int i = 0; i < thisTemplate.size(); i++) {
+ if (m->control_pressed) { return thisTemplate; }
+
+ string rightFrag = thisTemplate[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(thisTemplate[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+ databaseRight->setNumSeqs(thisTemplate.size());
+
+#else
+
+
+ for (int i = 0; i < thisTemplate.size(); i++) {
+
+ if (m->control_pressed) { return thisTemplate; }
+
+ string leftFrag = thisTemplate[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(thisTemplate[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(thisTemplate.size());
+
+ for (int i = 0; i < thisTemplate.size(); i++) {
+ if (m->control_pressed) { return thisTemplate; }
+
+ string rightFrag = thisTemplate[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(thisTemplate[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+ databaseRight->setNumSeqs(thisTemplate.size());
+#endif
+ }else if (searchMethod == "blast") {
+
+ //generate blastdb
+ databaseLeft = new BlastDB(-1.0, -1.0, 1, -3);
+
+ for (int i = 0; i < thisTemplate.size(); i++) { if (m->control_pressed) { return thisTemplate; } databaseLeft->addSequence(*thisTemplate[i]); }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(thisTemplate.size());
+ }
+
+ return thisTemplate;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getTemplate");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+ChimeraSlayer::~ChimeraSlayer() {
+ delete decalc;
+ if (templateFileName != "self") {
+ if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; }
+ else if (searchMethod == "blast") { delete databaseLeft; }
+ }
+}
+//***************************************************************************************************************
+void ChimeraSlayer::printHeader(ostream& out) {
+ m->mothurOutEndLine();
+ m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
+ m->mothurOutEndLine();
+
+ out << "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
+}
+//***************************************************************************************************************
+Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) {
+ try {
+ Sequence* trim = NULL;
+ if (trimChimera) { trim = trimQuery; }
+
+ 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)) {
+ m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine();
+ outAcc << querySeq->getName() << endl;
+
+ if (trimChimera) {
+ int lengthLeft = spotMap[chimeraResults[0].winLEnd] - spotMap[chimeraResults[0].winLStart];
+ int lengthRight = spotMap[chimeraResults[0].winREnd] - spotMap[chimeraResults[0].winRStart];
+
+ string newAligned = trim->getAligned();
+
+ if (lengthLeft > lengthRight) { //trim right
+ for (int i = (spotMap[chimeraResults[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //trim left
+ for (int i = 0; i < spotMap[chimeraResults[0].winLEnd]; i++) { newAligned[i] = '.'; }
+ }
+ trim->setAligned(newAligned);
}
+
}
+ }
+
+ printBlock(chimeraResults[0], chimeraFlag, out);
+ out << endl;
+ }else { out << querySeq->getName() << "\tno" << endl; }
+
+ return trim;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "print");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftPiece, data_results rightPiece) {
+ try {
+ Sequence* trim = NULL;
- for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) {
- Sequence* seq = getSequence(itDup->first); //makes copy so you can filter and mask and not effect template
+ if (trimChimera) {
+ string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned();
+ trim = new Sequence(leftPiece.trimQuery.getName(), aligned);
+ }
+
+ if ((leftPiece.flag == "yes") || (rightPiece.flag == "yes")) {
+
+ string chimeraFlag = "no";
+ if (leftPiece.flag == "yes") {
+
+ if( (leftPiece.results[0].bsa >= minBS && leftPiece.results[0].divr_qla_qrb >= divR)
+ ||
+ (leftPiece.results[0].bsb >= minBS && leftPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+ }
+
+ if (rightPiece.flag == "yes") {
+ if ( (rightPiece.results[0].bsa >= minBS && rightPiece.results[0].divr_qla_qrb >= divR)
+ ||
+ (rightPiece.results[0].bsb >= minBS && rightPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+ }
+
+ bool rightChimeric = false;
+ bool leftChimeric = false;
+
+ if (chimeraFlag == "yes") {
+ //which peice is chimeric or are both
+ if (rightPiece.flag == "yes") { if ((rightPiece.results[0].bsa >= minBS) || (rightPiece.results[0].bsb >= minBS)) { rightChimeric = true; } }
+ if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } }
+
+ if (rightChimeric || leftChimeric) {
+ m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine();
+ outAcc << querySeq->getName() << endl;
- SeqDist member;
- member.seq = seq;
- member.dist = itDup->second;
+ if (trimChimera) {
+ string newAligned = trim->getAligned();
+
+ //right side is fine so keep that
+ if ((leftChimeric) && (!rightChimeric)) {
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //both sides are chimeric, keep longest piece
+
+ int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLEnd] - leftPiece.spotMap[leftPiece.results[0].winLStart];
+ int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winREnd] - leftPiece.spotMap[leftPiece.results[0].winRStart];
+
+ int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4
+ int length = lengthLeftLeft;
+ if (lengthLeftLeft < lengthLeftRight) { longest = 2; length = lengthLeftRight; }
+
+ int lengthRightLeft = rightPiece.spotMap[rightPiece.results[0].winLEnd] - rightPiece.spotMap[rightPiece.results[0].winLStart];
+ int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winREnd] - rightPiece.spotMap[rightPiece.results[0].winRStart];
+
+ if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; }
+ if (lengthRightRight > length) { longest = 4; }
+
+ if (longest == 1) { //leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 2) { //leftright
+ //get rid of leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winLStart]-1); i < (leftPiece.spotMap[leftPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ //get rid of right
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 3) { //rightleft
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightright
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //rightright
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightleft
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < (rightPiece.spotMap[rightPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ }
+ }
+
+ trim->setAligned(newAligned);
+ }
- seqs.push_back(member);
}
+ }
+
+ printBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag, out);
+ out << endl;
+ }else { out << querySeq->getName() << "\tno" << endl; }
+
+ return trim;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "print");
+ exit(1);
+ }
+}
+
+#ifdef USE_MPI
+//***************************************************************************************************************
+Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results leftPiece, data_results rightPiece) {
+ try {
+ MPI_Status status;
+ bool results = false;
+ string outAccString = "";
+ string outputString = "";
+
+ Sequence* trim = NULL;
+
+ if (trimChimera) {
+ string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned();
+ trim = new Sequence(leftPiece.trimQuery.getName(), aligned);
+ }
+
+
+ if ((leftPiece.flag == "yes") || (rightPiece.flag == "yes")) {
+
+ string chimeraFlag = "no";
+ if (leftPiece.flag == "yes") {
+
+ if( (leftPiece.results[0].bsa >= minBS && leftPiece.results[0].divr_qla_qrb >= divR)
+ ||
+ (leftPiece.results[0].bsb >= minBS && leftPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+ }
+
+ if (rightPiece.flag == "yes") {
+ if ( (rightPiece.results[0].bsa >= minBS && rightPiece.results[0].divr_qla_qrb >= divR)
+ ||
+ (rightPiece.results[0].bsb >= minBS && rightPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+ }
+
+ bool rightChimeric = false;
+ bool leftChimeric = false;
+
+ if (chimeraFlag == "yes") {
+ //which peice is chimeric or are both
+ if (rightPiece.flag == "yes") { if ((rightPiece.results[0].bsa >= minBS) || (rightPiece.results[0].bsb >= minBS)) { rightChimeric = true; } }
+ if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } }
- //limit number of parents to explore - default 5
- if (Results.size() > parents) {
- //sort by distance
- sort(seqs.begin(), seqs.end(), compareSeqDist);
- //prioritize larger more similiar sequence fragments
- reverse(seqs.begin(), seqs.end());
+ if (rightChimeric || leftChimeric) {
+ cout << querySeq->getName() << "\tyes" << endl;
+ outAccString += querySeq->getName() + "\n";
+ results = true;
- for (int k = seqs.size()-1; k > (parents-1); k--) {
- delete seqs[k].seq;
- seqs.pop_back();
+ //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;
+
+ if (trimChimera) {
+ string newAligned = trim->getAligned();
+
+ //right side is fine so keep that
+ if ((leftChimeric) && (!rightChimeric)) {
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //both sides are chimeric, keep longest piece
+
+ int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLEnd] - leftPiece.spotMap[leftPiece.results[0].winLStart];
+ int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winREnd] - leftPiece.spotMap[leftPiece.results[0].winRStart];
+
+ int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4
+ int length = lengthLeftLeft;
+ if (lengthLeftLeft < lengthLeftRight) { longest = 2; length = lengthLeftRight; }
+
+ int lengthRightLeft = rightPiece.spotMap[rightPiece.results[0].winLEnd] - rightPiece.spotMap[rightPiece.results[0].winLStart];
+ int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winREnd] - rightPiece.spotMap[rightPiece.results[0].winRStart];
+
+ if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; }
+ if (lengthRightRight > length) { longest = 4; }
+
+ if (longest == 1) { //leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 2) { //leftright
+ //get rid of leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winLStart]-1); i < (leftPiece.spotMap[leftPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ //get rid of right
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 3) { //rightleft
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightright
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //rightright
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightleft
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < (rightPiece.spotMap[rightPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ }
+ }
+
+ trim->setAligned(newAligned);
}
+
}
+ }
+
+ outputString = getBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag);
+ outputString += "\n";
- //put seqs into vector to send to slayer
- vector<Sequence*> seqsForSlayer;
- for (int k = 0; k < seqs.size(); k++) { seqsForSlayer.push_back(seqs[k].seq); }
-//ofstream out;
-//string name = querySeqs[i]->getName();
-//cout << name << endl;
-//name = name.substr(name.find_first_of("|")+1);
-//cout << name << endl;
-//name = name.substr(name.find_first_of("|")+1);
-//cout << name << endl;
-//name = name.substr(0, name.find_last_of("|"));
-//cout << name << endl;
-//string filename = name + ".seqsforslayer";
-//openOutputFile(filename, out);
-//for (int u = 0; u < seqsForSlayer.size(); u++) { seqsForSlayer[u]->printSequence(out); }
-//out.close();
-//filename = name + ".fasta";
-//openOutputFile(filename, out);
-//q->printSequence(out);
-//out.close();
+ //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;
+ }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 trim;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "print");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
+ try {
+ MPI_Status status;
+ bool results = false;
+ string outAccString = "";
+ string outputString = "";
+
+ Sequence* trim = NULL;
+ if (trimChimera) { trim = trimQuery; }
+
+ 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"; }
- //mask then send to slayer...
- if (seqMask != "") {
- decalc->setMask(seqMask);
-
- //mask querys
- decalc->runMask(querySeqs[i]);
+
+ if (chimeraFlag == "yes") {
+ if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
+ cout << querySeq->getName() << "\tyes" << endl;
+ outAccString += querySeq->getName() + "\n";
+ results = true;
- //mask parents
- for (int k = 0; k < seqsForSlayer.size(); k++) {
- decalc->runMask(seqsForSlayer[k]);
- }
+ //write to accnos file
+ int length = outAccString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outAccString.c_str(), length);
- for (int i = 0; i < numSeqs; i++) {
- spotMap[i] = decalc->getMaskMap();
+ MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+
+ if (trimChimera) {
+ int lengthLeft = spotMap[chimeraResults[0].winLEnd] - spotMap[chimeraResults[0].winLStart];
+ int lengthRight = spotMap[chimeraResults[0].winREnd] - spotMap[chimeraResults[0].winRStart];
+
+ string newAligned = trim->getAligned();
+ if (lengthLeft > lengthRight) { //trim right
+ for (int i = (spotMap[chimeraResults[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //trim left
+ for (int i = 0; i < (spotMap[chimeraResults[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ }
+ trim->setAligned(newAligned);
}
+ }
+ }
+
+ outputString = getBlock(chimeraResults[0], chimeraFlag);
+ outputString += "\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;
+
+ }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 trim;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "print");
+ exit(1);
+ }
+}
+#endif
+
+//***************************************************************************************************************
+int ChimeraSlayer::getChimeras(Sequence* query) {
+ try {
+ if (trimChimera) { trimQuery = new Sequence(query->getName(), query->getAligned()); printResults.trimQuery = *trimQuery; }
+
+ chimeraFlags = "no";
+ printResults.flag = "no";
+
+ //filter query
+ spotMap = runFilter(query);
+ printResults.spotMap = spotMap;
+
+ querySeq = query;
+
+ //you must create a template
+ vector<Sequence*> thisTemplate;
+ if (templateFileName != "self") { thisTemplate = templateSeqs; }
+ else { thisTemplate = getTemplate(query); } //fills thistemplate and creates the databases
+
+ if (m->control_pressed) { return 0; }
+
+ if (thisTemplate.size() == 0) { return 0; } //not chimeric
+
+ //referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity
+ Maligner maligner(thisTemplate, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
+ Slayer slayer(window, increment, minSim, divR, iters, minSNP);
+
+ if (templateFileName == "self") {
+ if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; }
+ else if (searchMethod == "blast") { delete databaseLeft; }
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ string chimeraFlag = maligner.getResults(query, decalc);
+ if (m->control_pressed) { return 0; }
+ vector<results> Results = maligner.getOutput();
+
+ //found in testing realigning only made things worse
+ if (realign) {
+ ChimeraReAligner realigner(thisTemplate, match, misMatch);
+ realigner.reAlign(query, Results);
+ }
+ if (chimeraFlag == "yes") {
+
+ //get sequence that were given from maligner results
+ vector<SeqDist> seqs;
+ map<string, float> removeDups;
+ map<string, float>::iterator itDup;
+ map<string, string> parentNameSeq;
+ map<string, string>::iterator itSeq;
+ for (int j = 0; j < Results.size(); j++) {
+ float dist = (Results[j].regionEnd - Results[j].regionStart + 1) * Results[j].queryToParentLocal;
+ //only add if you are not a duplicate
+ itDup = removeDups.find(Results[j].parent);
+ if (itDup == removeDups.end()) { //this is not duplicate
+ removeDups[Results[j].parent] = dist;
+ parentNameSeq[Results[j].parent] = Results[j].parentAligned;
+ }else if (dist > itDup->second) { //is this a stronger number for this parent
+ removeDups[Results[j].parent] = dist;
+ parentNameSeq[Results[j].parent] = Results[j].parentAligned;
}
+ }
+
+ for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) {
+ itSeq = parentNameSeq.find(itDup->first);
+ Sequence* seq = new Sequence(itDup->first, itSeq->second);
+
+ SeqDist member;
+ member.seq = seq;
+ member.dist = itDup->second;
- //send to slayer
- chimeraFlags[i] = slayer->getResults(querySeqs[i], seqsForSlayer);
- chimeraResults[i] = slayer->getOutput();
+ seqs.push_back(member);
+ }
- //free memory
- for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
- //}
+ //limit number of parents to explore - default 3
+ if (Results.size() > parents) {
+ //sort by distance
+ sort(seqs.begin(), seqs.end(), compareSeqDist);
+ //prioritize larger more similiar sequence fragments
+ reverse(seqs.begin(), seqs.end());
+
+ for (int k = seqs.size()-1; k > (parents-1); k--) {
+ delete seqs[k].seq;
+ seqs.pop_back();
+ }
+ }
- }
- //free memory
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; }
-
- if (seqMask != "") {
- delete decalc;
+ //put seqs into vector to send to slayer
+ vector<Sequence*> seqsForSlayer;
+
+ for (int k = 0; k < seqs.size(); k++) { seqsForSlayer.push_back(seqs[k].seq); }
+
+ //mask then send to slayer...
+ if (seqMask != "") {
+ decalc->setMask(seqMask);
+
+ //mask querys
+ decalc->runMask(query);
+
+ //mask parents
+ for (int k = 0; k < seqsForSlayer.size(); k++) {
+ decalc->runMask(seqsForSlayer[k]);
+ }
+
+ spotMap = decalc->getMaskMap();
+ }
+
+ if (m->control_pressed) { for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } return 0; }
+
+ //send to slayer
+ chimeraFlags = slayer.getResults(query, seqsForSlayer);
+ if (m->control_pressed) { return 0; }
+ chimeraResults = slayer.getOutput();
+
+ //free memory
+ for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
+
+ printResults.spotMap = spotMap;
+ printResults.flag = chimeraFlags;
+ printResults.results = chimeraResults;
}
return 0;
}
catch(exception& e) {
- errorOut(e, "ChimeraSlayer", "getChimeras");
+ m->errorOut(e, "ChimeraSlayer", "getChimeras");
exit(1);
}
}
//***************************************************************************************************************
-Sequence* ChimeraSlayer::getSequence(string name) {
- try{
- Sequence* temp;
+void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
+ try {
+ out << querySeq->getName() << '\t';
+ out << data.parentA.getName() << "\t" << data.parentB.getName() << '\t';
+
+ out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t';
+ out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t';
+
+ out << flag << '\t' << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "printBlock");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+void ChimeraSlayer::printBlock(data_results leftdata, data_results rightdata, bool leftChimeric, bool rightChimeric, string flag, ostream& out){
+ try {
+
+ if ((leftChimeric) && (!rightChimeric)) { //print left
+ out << querySeq->getName() << '\t';
+ out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t';
+
+ out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t';
+ out << leftdata.results[0].divr_qlb_qra << '\t' << leftdata.results[0].qlb_qra << '\t' << leftdata.results[0].bsb << '\t';
+
+ out << flag << '\t' << leftdata.spotMap[leftdata.results[0].winLStart] << "-" << leftdata.spotMap[leftdata.results[0].winLEnd] << '\t' << leftdata.spotMap[leftdata.results[0].winRStart] << "-" << leftdata.spotMap[leftdata.results[0].winREnd] << '\t';
+
+ }else if ((!leftChimeric) && (rightChimeric)) { //print right
+ out << querySeq->getName() << '\t';
+ out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t';
+
+ out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t';
+ out << rightdata.results[0].divr_qlb_qra << '\t' << rightdata.results[0].qlb_qra << '\t' << rightdata.results[0].bsb << '\t';
+
+ out << flag << '\t' << rightdata.spotMap[rightdata.results[0].winLStart] << "-" << rightdata.spotMap[rightdata.results[0].winLEnd] << '\t' << rightdata.spotMap[rightdata.results[0].winRStart] << "-" << rightdata.spotMap[rightdata.results[0].winREnd] << '\t';
+
+ }else { //print both results
+ if (leftdata.flag == "yes") {
+ out << querySeq->getName() + "_LEFT" << '\t';
+ out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t';
+
+ out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t';
+ out << leftdata.results[0].divr_qlb_qra << '\t' << leftdata.results[0].qlb_qra << '\t' << leftdata.results[0].bsb << '\t';
+
+ out << flag << '\t' << leftdata.spotMap[leftdata.results[0].winLStart] << "-" << leftdata.spotMap[leftdata.results[0].winLEnd] << '\t' << leftdata.spotMap[leftdata.results[0].winRStart] << "-" << leftdata.spotMap[leftdata.results[0].winREnd] << '\t';
+ }
+
+ if (rightdata.flag == "yes") {
+ if (leftdata.flag == "yes") { out << endl; }
+
+ out << querySeq->getName() + "_RIGHT"<< '\t';
+ out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t';
+
+ out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t';
+ out << rightdata.results[0].divr_qlb_qra << '\t' << rightdata.results[0].qlb_qra << '\t' << rightdata.results[0].bsb << '\t';
+
+ out << flag << '\t' << rightdata.spotMap[rightdata.results[0].winLStart] << "-" << rightdata.spotMap[rightdata.results[0].winLEnd] << '\t' << rightdata.spotMap[rightdata.results[0].winRStart] << "-" << rightdata.spotMap[rightdata.results[0].winREnd] << '\t';
- //look through templateSeqs til you find it
- int spot = -1;
- for (int i = 0; i < templateSeqs.size(); i++) {
- if (name == templateSeqs[i]->getName()) {
- spot = i;
- break;
}
}
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "printBlock");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+string ChimeraSlayer::getBlock(data_results leftdata, data_results rightdata, bool leftChimeric, bool rightChimeric, string flag){
+ try {
- if(spot == -1) { mothurOut("Error: Could not find sequence in chimeraSlayer."); mothurOutEndLine(); return NULL; }
+ string out = "";
+
+ if ((leftChimeric) && (!rightChimeric)) { //get left
+ out += querySeq->getName() + "\t";
+ out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t";
+
+ out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t";
+ out += toString(leftdata.results[0].divr_qlb_qra) + "\t" + toString(leftdata.results[0].qlb_qra) + "\t" + toString(leftdata.results[0].bsb) + "\t";
+
+ out += flag + "\t" + toString(leftdata.spotMap[leftdata.results[0].winLStart]) + "-" + toString(leftdata.spotMap[leftdata.results[0].winLEnd]) + "\t" + toString(leftdata.spotMap[leftdata.results[0].winRStart]) + "-" + toString(leftdata.spotMap[leftdata.results[0].winREnd]) + "\t";
+
+ }else if ((!leftChimeric) && (rightChimeric)) { //print right
+ out += querySeq->getName() + "\t";
+ out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t";
+
+ out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t";
+ out += toString(rightdata.results[0].divr_qlb_qra) + "\t" + toString(rightdata.results[0].qlb_qra) + "\t" + toString(rightdata.results[0].bsb) + "\t";
+
+ out += flag + "\t" + toString(rightdata.spotMap[rightdata.results[0].winLStart]) + "-" + toString(rightdata.spotMap[rightdata.results[0].winLEnd]) + "\t" + toString(rightdata.spotMap[rightdata.results[0].winRStart]) + "-" + toString(rightdata.spotMap[rightdata.results[0].winREnd]) + "\t";
+
+ }else { //print both results
+
+ if (leftdata.flag == "yes") {
+ out += querySeq->getName() + "_LEFT\t";
+ out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t";
+
+ out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t";
+ out += toString(leftdata.results[0].divr_qlb_qra) + "\t" + toString(leftdata.results[0].qlb_qra) + "\t" + toString(leftdata.results[0].bsb) + "\t";
+
+ out += flag + "\t" + toString(leftdata.spotMap[leftdata.results[0].winLStart]) + "-" + toString(leftdata.spotMap[leftdata.results[0].winLEnd]) + "\t" + toString(leftdata.spotMap[leftdata.results[0].winRStart]) + "-" + toString(leftdata.spotMap[leftdata.results[0].winREnd]) + "\t";
+ }
+
+ if (rightdata.flag == "yes") {
+ if (leftdata.flag == "yes") { out += "\n"; }
+ out += querySeq->getName() + "_RIGHT\t";
+ out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t";
+
+ out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t";
+ out += toString(rightdata.results[0].divr_qlb_qra) + "\t" + toString(rightdata.results[0].qlb_qra) + "\t" + toString(rightdata.results[0].bsb) + "\t";
+
+ out += flag + "\t" + toString(rightdata.spotMap[rightdata.results[0].winLStart]) + "-" + toString(rightdata.spotMap[rightdata.results[0].winLEnd]) + "\t" + toString(rightdata.spotMap[rightdata.results[0].winRStart]) + "-" + toString(rightdata.spotMap[rightdata.results[0].winREnd]) + "\t";
+ }
+ }
- temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
+ return out;
- return temp;
}
catch(exception& e) {
- errorOut(e, "ChimeraSlayer", "getSequence");
+ m->errorOut(e, "ChimeraSlayer", "getBlock");
exit(1);
}
}
//***************************************************************************************************************
-void ChimeraSlayer::printBlock(data_struct data, ostream& out, int i){
+string ChimeraSlayer::getBlock(data_struct data, string flag){
try {
- out << "parentA: " << data.parentA.getName() << " parentB: " << data.parentB.getName() << endl;
- out << "Left Window: " << spotMap[i][data.winLStart] << " " << spotMap[i][data.winLEnd] << endl;
- out << "Right Window: " << spotMap[i][data.winRStart] << " " << spotMap[i][data.winREnd] << endl;
-
- out << "Divergence of Query to Leftside ParentA and Rightside ParentB: " << data.divr_qla_qrb << '\t' << "Bootstrap: " << data.bsa << endl;
- out << "Divergence of Query to Rightside ParentA and Leftside ParentB: " << data.divr_qlb_qra << '\t' << "Bootstrap: " << data.bsb << endl;
+ string outputString = "";
- out << "Similarity of parents: " << data.ab << endl;
- out << "Similarity of query to parentA: " << data.qa << endl;
- out << "Similarity of query to parentB: " << data.qb << endl;
+ 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";
- //out << "Per_id(QL,A): " << data.qla << endl;
- //out << "Per_id(QL,B): " << data.qlb << endl;
- //out << "Per_id(QR,A): " << data.qra << endl;
- //out << "Per_id(QR,B): " << data.qrb << endl;
-
+ outputString += flag + "\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
- out << "DeltaL: " << (data.qla - data.qlb) << endl;
- out << "DeltaR: " << (data.qra - data.qrb) << endl;
-
+ return outputString;
}
catch(exception& e) {
- errorOut(e, "ChimeraSlayer", "printBlock");
+ m->errorOut(e, "ChimeraSlayer", "getBlock");
exit(1);
}
}
-//***************************************************************************************************************
+//***************************************************************************************************************/
projects / mothur.git / blobdiff