//m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
path = m->argv;
- path = path.substr(0, (path.find_last_of('m')));
+ string tempPath = path;
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
struct data_results {
vector<data_struct> results;
string flag;
- map<int, int> spotMap;
Sequence trimQuery;
+ //results malignerResults;
- data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), spotMap(s), trimQuery(t) {}
+ data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), trimQuery(t) {}
data_results() {}
};
/***********************************************************************/
public:
Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
- virtual ~Chimera(){ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } };
+ virtual ~Chimera(){ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } for (int i = 0; i < filteredTemplateSeqs.size(); i++) { delete filteredTemplateSeqs[i]; } };
virtual bool getUnaligned() { return unaligned; }
virtual int getLength() { return length; }
virtual vector<Sequence*> readSeqs(string);
protected:
vector<Sequence*> templateSeqs;
+ vector<Sequence*> filteredTemplateSeqs;
bool filter, unaligned;
int length;
string seqMask, filterString, outputDir, templateFileName;
//make sure you don't cutoff end of query
if (parents[parents.size()-1].nastRegionEnd < (qAligned.length()-1)) { newQuery += qAligned.substr(parents[parents.size()-1].nastRegionEnd+1); }
- //set query to new aligned string
query->setAligned(newQuery);
//free memory
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]); }
+ //run filter on template copying templateSeqs into filteredTemplateSeqs
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
+ filteredTemplateSeqs.push_back(newSeq);
+ runFilter(newSeq);
+ }
}
string kmerDBNameLeft;
string kmerDBNameRight;
}
}
//***************************************************************************************************************
-vector<Sequence*> ChimeraSlayer::getTemplate(Sequence* q) {
+vector<Sequence*> ChimeraSlayer::getTemplate(Sequence* q, vector<Sequence*>& userTemplateFiltered) {
try {
//when template=self, the query file is sorted from most abundance to least abundant
if (!(priority[templateSeqs[i]->getName()] > myAbund)) { break; }
//if its am not chimeric add it
- if (chimericSeqs.count(templateSeqs[i]->getName()) == 0) { userTemplate.push_back(templateSeqs[i]); }
+ if (chimericSeqs.count(templateSeqs[i]->getName()) == 0) {
+ userTemplate.push_back(templateSeqs[i]);
+ if (searchMethod == "distance") { userTemplateFiltered.push_back(filteredTemplateSeqs[i]); }
+ }
}
string kmerDBNameLeft;
if (templateFileName == "self") { chimericSeqs.insert(querySeq->getName()); }
if (trimChimera) {
- int lengthLeft = spotMap[chimeraResults[0].winLEnd] - spotMap[chimeraResults[0].winLStart];
- int lengthRight = spotMap[chimeraResults[0].winREnd] - spotMap[chimeraResults[0].winRStart];
+ int lengthLeft = chimeraResults[0].winLEnd - chimeraResults[0].winLStart;
+ int lengthRight = chimeraResults[0].winREnd - 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] = '.'; }
+ for (int i = (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] = '.'; }
+ for (int i = 0; i < chimeraResults[0].winLEnd; i++) { newAligned[i] = '.'; }
}
trim->setAligned(newAligned);
}
//right side is fine so keep that
if ((leftChimeric) && (!rightChimeric)) {
- for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ for (int i = 0; i < 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] = '.'; }
+ for (int i = (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 lengthLeftLeft = leftPiece.results[0].winLEnd - leftPiece.results[0].winLStart;
+ int lengthLeftRight = leftPiece.results[0].winREnd - 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];
+ int lengthRightLeft = rightPiece.results[0].winLEnd - rightPiece.results[0].winLStart;
+ int lengthRightRight = rightPiece.results[0].winREnd - 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] = '.'; }
+ for (int i = (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] = '.'; }
+ for (int i = (leftPiece.results[0].winLStart-1); i < (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] = '.'; }
+ for (int i = (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] = '.'; }
+ for (int i = 0; i < 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] = '.'; }
+ for (int i = (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] = '.'; }
+ for (int i = 0; i < 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] = '.'; }
+ for (int i = (rightPiece.results[0].winLStart-1); i < (rightPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; }
}
}
//right side is fine so keep that
if ((leftChimeric) && (!rightChimeric)) {
- for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ for (int i = 0; i < 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] = '.'; }
+ for (int i = (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 lengthLeftLeft = leftPiece.results[0].winLEnd - leftPiece.results[0].winLStart;
+ int lengthLeftRight = leftPiece.results[0].winREnd - 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];
+ int lengthRightLeft = rightPiece.results[0].winLEnd - rightPiece.results[0].winLStart;
+ int lengthRightRight = rightPiece.results[0].winREnd - 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] = '.'; }
+ for (int i = (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] = '.'; }
+ for (int i = (leftPiece.results[0].winLStart-1); i < (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] = '.'; }
+ for (int i = (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] = '.'; }
+ for (int i = 0; i < 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] = '.'; }
+ for (int i = (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] = '.'; }
+ for (int i = 0; i < 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] = '.'; }
+ for (int i = (rightPiece.results[0].winLStart-1); i < (rightPiece.results[0].winLEnd-1); i++) { newAligned[i] = '.'; }
}
}
delete buf2;
if (trimChimera) {
- int lengthLeft = spotMap[chimeraResults[0].winLEnd] - spotMap[chimeraResults[0].winLStart];
- int lengthRight = spotMap[chimeraResults[0].winREnd] - spotMap[chimeraResults[0].winRStart];
+ int lengthLeft = chimeraResults[0].winLEnd - chimeraResults[0].winLStart;
+ int lengthRight = chimeraResults[0].winREnd - 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] = '.'; }
+ for (int i = (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] = '.'; }
+ for (int i = 0; i < (chimeraResults[0].winLEnd-1); i++) { newAligned[i] = '.'; }
}
trim->setAligned(newAligned);
}
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 this template and creates the databases
+ vector<Sequence*> thisFilteredTemplate;
+ if (templateFileName != "self") { thisTemplate = templateSeqs; thisFilteredTemplate = filteredTemplateSeqs; }
+ else { thisTemplate = getTemplate(query, thisFilteredTemplate); } //fills this template 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);
+ //moved this out of maligner - 4/29/11
+ vector<Sequence*> refSeqs = getRefSeqs(query, thisTemplate, thisFilteredTemplate);
+
+ Maligner maligner(refSeqs, match, misMatch, divR, minSim, minCov);
+ Slayer slayer(window, increment, minSim, divR, iters, minSNP, minBS);
if (templateFileName == "self") {
if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; }
vector<results> Results = maligner.getOutput();
- //cout << query->getName() << endl;
- //for (int i = 0; i < Results.size(); i++) {
- //cout << Results[i].parent << '\t' << Results[i].regionStart << '\t' << Results[i].regionEnd << '\t' << Results[i].nastRegionStart << '\t' << Results[i].nastRegionEnd << '\t' << Results[i].queryToParent << '\t' << Results[i].queryToParentLocal << endl;
- //}
- //cout << "done\n" << endl;
+ for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
+
if (chimeraFlag == "yes") {
if (realign) {
//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
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;
+
+ //free memory
+ for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
}
return 0;
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';
+ out << flag << '\t' << data.winLStart << "-" << data.winLEnd << '\t' << data.winRStart << "-" << data.winREnd << '\t';
}
catch(exception& e) {
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';
+ out << flag << '\t' << leftdata.results[0].winLStart << "-" << leftdata.results[0].winLEnd << '\t' << leftdata.results[0].winRStart << "-" << leftdata.results[0].winREnd << '\t';
}else if ((!leftChimeric) && (rightChimeric)) { //print right
out << querySeq->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';
+ out << flag << '\t' << rightdata.results[0].winLStart << "-" << rightdata.results[0].winLEnd << '\t' << rightdata.results[0].winRStart << "-" << rightdata.results[0].winREnd << '\t';
}else { //print both results
if (leftdata.flag == "yes") {
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';
+ out << flag << '\t' << leftdata.results[0].winLStart << "-" << leftdata.results[0].winLEnd << '\t' << leftdata.results[0].winRStart << "-" << leftdata.results[0].winREnd << '\t';
}
if (rightdata.flag == "yes") {
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';
+ out << flag << '\t' << rightdata.results[0].winLStart << "-" << rightdata.results[0].winLEnd << '\t' << rightdata.results[0].winRStart << "-" << rightdata.results[0].winREnd << '\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";
+ out += flag + "\t" + toString(leftdata.results[0].winLStart) + "-" + toString(leftdata.results[0].winLEnd) + "\t" + toString(leftdata.results[0].winRStart) + "-" + toString(leftdata.results[0].winREnd) + "\t";
}else if ((!leftChimeric) && (rightChimeric)) { //print right
out += querySeq->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";
+ out += flag + "\t" + toString(rightdata.results[0].winLStart) + "-" + toString(rightdata.results[0].winLEnd) + "\t" + toString(rightdata.results[0].winRStart) + "-" + toString(rightdata.results[0].winREnd) + "\t";
}else { //print both results
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";
+ out += flag + "\t" + toString(leftdata.results[0].winLStart) + "-" + toString(leftdata.results[0].winLEnd) + "\t" + toString(leftdata.results[0].winRStart) + "-" + toString(leftdata.results[0].winREnd) + "\t";
}
if (rightdata.flag == "yes") {
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";
+ out += flag + "\t" + toString(rightdata.results[0].winLStart) + "-" + toString(rightdata.results[0].winLEnd) + "\t" + toString(rightdata.results[0].winRStart) + "-" + toString(rightdata.results[0].winREnd) + "\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 += flag + "\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
+ outputString += flag + "\t" + toString(data.winLStart) + "-" + toString(data.winLEnd) + "\t" + toString(data.winRStart) + "-" + toString(data.winREnd) + "\t";
return outputString;
}
exit(1);
}
}
+//***************************************************************************************************************
+vector<Sequence*> ChimeraSlayer::getRefSeqs(Sequence* q, vector<Sequence*>& thisTemplate, vector<Sequence*>& thisFilteredTemplate){
+ try {
+
+ vector<Sequence*> refSeqs;
+
+ if (searchMethod == "distance") {
+ //find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate
+ Sequence* newSeq = new Sequence(q->getName(), q->getAligned());
+ runFilter(newSeq);
+ refSeqs = decalc->findClosest(newSeq, thisTemplate, thisFilteredTemplate, numWanted);
+ }else if (searchMethod == "blast") {
+ refSeqs = getBlastSeqs(q, thisTemplate, numWanted); //fills indexes
+ }else if (searchMethod == "kmer") {
+ refSeqs = getKmerSeqs(q, thisTemplate, numWanted); //fills indexes
+ }else { m->mothurOut("not valid search."); exit(1); } //should never get here
+
+ return refSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getRefSeqs");
+ exit(1);
+ }
+}
//***************************************************************************************************************/
+vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db, int num) {
+ try {
+
+ vector<Sequence*> refResults;
+
+ //get parts of query
+ string queryUnAligned = q->getUnaligned();
+ string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
+ string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
+
+ Sequence* queryLeft = new Sequence(q->getName()+"left", leftQuery);
+ Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
+
+ vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
+ vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
+
+ vector<int> smaller;
+ vector<int> larger;
+
+ if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight; larger = tempIndexesLeft; }
+ else { smaller = tempIndexesLeft; larger = tempIndexesRight; }
+
+ //merge results
+ map<int, int> seen;
+ map<int, int>::iterator it;
+ vector<int> mergedResults;
+ for (int i = 0; i < smaller.size(); i++) {
+ //add left if you havent already
+ it = seen.find(smaller[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(smaller[i]);
+ seen[smaller[i]] = smaller[i];
+ }
+
+ //add right if you havent already
+ it = seen.find(larger[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(larger[i]);
+ seen[larger[i]] = larger[i];
+ }
+ }
+
+ for (int i = smaller.size(); i < larger.size(); i++) {
+ //add right if you havent already
+ it = seen.find(larger[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(larger[i]);
+ seen[larger[i]] = larger[i];
+ }
+ }
+ //numWanted = mergedResults.size();
+
+ //cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted << endl;
+ for (int i = 0; i < mergedResults.size(); i++) {
+ //cout << db[mergedResults[i]]->getName() << '\t' << mergedResults[i] << endl;
+
+ if (db[mergedResults[i]]->getName() != q->getName()) {
+ Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
+ refResults.push_back(temp);
+ //cout << db[mergedResults[i]]->getName() << endl;
+ }
+
+ //cout << mergedResults[i] << endl;
+ }
+ //cout << "done " << q->getName() << endl;
+ delete queryRight;
+ delete queryLeft;
+
+ return refResults;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getBlastSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<Sequence*> ChimeraSlayer::getKmerSeqs(Sequence* q, vector<Sequence*>& db, int num) {
+ try {
+
+ //get parts of query
+ string queryUnAligned = q->getUnaligned();
+ string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
+ string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
+
+ Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
+ Sequence* queryRight = new Sequence(q->getName(), rightQuery);
+
+ vector<int> tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, numWanted);
+ vector<int> tempIndexesRight = databaseRight->findClosestSequences(queryRight, numWanted);
+
+ //merge results
+ map<int, int> seen;
+ map<int, int>::iterator it;
+ vector<int> mergedResults;
+ for (int i = 0; i < tempIndexesLeft.size(); i++) {
+ //add left if you havent already
+ it = seen.find(tempIndexesLeft[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(tempIndexesLeft[i]);
+ seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
+ }
+
+ //add right if you havent already
+ it = seen.find(tempIndexesRight[i]);
+ if (it == seen.end()) {
+ mergedResults.push_back(tempIndexesRight[i]);
+ seen[tempIndexesRight[i]] = tempIndexesRight[i];
+ }
+ }
+
+ //numWanted = mergedResults.size();
+
+ //cout << q->getName() << endl;
+ vector<Sequence*> refResults;
+ for (int i = 0; i < mergedResults.size(); i++) {
+ //cout << db[mergedResults[i]]->getName() << endl;
+ if (db[mergedResults[i]]->getName() != q->getName()) {
+ Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
+ refResults.push_back(temp);
+ }
+ }
+ //cout << endl;
+ delete queryRight;
+ delete queryLeft;
+
+ return refResults;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getKmerSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
Sequence* querySeq;
Sequence trimQuery;
DeCalculator* decalc;
- map<int, int> spotMap;
Database* databaseRight;
Database* databaseLeft;
map<string, int> priority; //for template=self, seqname, seqAligned, abundance
set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
-
+
vector<data_struct> chimeraResults;
data_results printResults;
string chimeraFlags, searchMethod, fastafile;
string getBlock(data_struct, string);
string getBlock(data_results, data_results, bool, bool, string);
//int readNameFile(string);
- vector<Sequence*> getTemplate(Sequence*);
+ vector<Sequence*> getTemplate(Sequence*, vector<Sequence*>&);
+ vector<Sequence*> getRefSeqs(Sequence*, vector<Sequence*>&, vector<Sequence*>&);
+ vector<Sequence*> getBlastSeqs(Sequence*, vector<Sequence*>&, int);
+ vector<Sequence*> getKmerSeqs(Sequence*, vector<Sequence*>&, int);
};
temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
convert(temp, parents);
- temp = validParameter.validFile(parameters, "realign", true); if (temp == "not found") { temp = "t"; }
+ temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "t"; }
realign = m->isTrue(temp);
temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; }
int ChimeraSlayerCommand::execute(){
try{
-
if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {
}
//***************************************************************************************************************
//gets closest matches to each end, since chimeras will most likely have different parents on each end
-vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*> db, int& numWanted, vector<int>& indexes) {
+vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*>& thisTemplate, vector<Sequence*>& thisFilteredTemplate, int& numWanted) {
try {
- indexes.clear();
+ //indexes.clear();
vector<Sequence*> seqsMatches;
Sequence queryRight(querySeq->getName(), rightQuery);
//cout << querySeq->getName() << '\t' << leftSpot << '\t' << rightSpot << '\t' << firstBaseSpot << '\t' << lastBaseSpot << endl;
//cout << queryUnAligned.length() << '\t' << queryLeft.getUnaligned().length() << '\t' << queryRight.getUnaligned().length() << endl;
- for(int j = 0; j < db.size(); j++){
+ for(int j = 0; j < thisFilteredTemplate.size(); j++){
- string dbAligned = db[j]->getAligned();
+ string dbAligned = thisFilteredTemplate[j]->getAligned();
string leftDB = dbAligned.substr(firstBaseSpot, (leftSpot-firstBaseSpot+1)); //first 1/3 of the sequence
string rightDB = dbAligned.substr(rightSpot, (lastBaseSpot-rightSpot)); //last 1/3 of the sequence
- Sequence dbLeft(db[j]->getName(), leftDB);
- Sequence dbRight(db[j]->getName(), rightDB);
+ Sequence dbLeft(thisFilteredTemplate[j]->getName(), leftDB);
+ Sequence dbRight(thisFilteredTemplate[j]->getName(), rightDB);
distcalculator->calcDist(queryLeft, dbLeft);
float distLeft = distcalculator->getDist();
//sort by smallest distance
sort(distsRight.begin(), distsRight.end(), compareSeqDist);
sort(distsLeft.begin(), distsLeft.end(), compareSeqDist);
-// cout << distsLeft.size() << '\t' << distsRight.size() << endl;
-// for(int i=0;i<15;i++){
-// cout << "left\t" << db[distsLeft[i].index]->getName() << '\t' << distsLeft[i].dist << endl;
-// }
-// for(int i=0;i<15;i++){
-// cout << "right\t" << db[distsLeft[i].index]->getName() << '\t' << distsRight[i].dist << endl;
-// }
-
//merge results
map<string, string> seen;
//int lasti = 0;
for (int i = 0; i < numWanted+1; i++) {
//add left if you havent already
- it = seen.find(db[distsLeft[i].index]->getName());
+ it = seen.find(thisTemplate[distsLeft[i].index]->getName());
if (it == seen.end()) {
dists.push_back(distsLeft[i]);
- seen[db[distsLeft[i].index]->getName()] = db[distsLeft[i].index]->getName();
+ seen[thisTemplate[distsLeft[i].index]->getName()] = thisTemplate[distsLeft[i].index]->getName();
lastLeft = distsLeft[i].dist;
// cout << "loop-left\t" << db[distsLeft[i].index]->getName() << '\t' << distsLeft[i].dist << endl;
}
//add right if you havent already
- it = seen.find(db[distsRight[i].index]->getName());
+ it = seen.find(thisTemplate[distsRight[i].index]->getName());
if (it == seen.end()) {
dists.push_back(distsRight[i]);
- seen[db[distsRight[i].index]->getName()] = db[distsRight[i].index]->getName();
+ seen[thisTemplate[distsRight[i].index]->getName()] = thisTemplate[distsRight[i].index]->getName();
lastRight = distsRight[i].dist;
// cout << "loop-right\t" << db[distsRight[i].index]->getName() << '\t' << distsRight[i].dist << endl;
}
- //if (dists.size() > numWanted) { lasti = i; break; } //you have enough results
}
-// cout << "lastLeft\t" << lastLeft << endl;
-
- //add in sequences with same distance as last sequence added
- /* lasti++;
- int i = lasti;
- while (i < distsLeft.size()) {
- if (distsLeft[i].dist == lastLeft) {
- it = seen.find(db[distsLeft[i].index]->getName());
- if (it == seen.end()) {
-// cout << "newLoop-left\t" << db[distsLeft[i].index]->getName() << '\t' << distsLeft[i].dist << endl;
- dists.push_back(distsLeft[i]);
- seen[db[distsRight[i].index]->getName()] = db[distsLeft[i].index]->getName();
-// numWanted++;
- }
- }
- else { break; }
- i++;
- }
-
-// cout << "lastRight\t" << lastRight << endl;
- //add in sequences with same distance as last sequence added
- i = lasti;
- while (i < distsRight.size()) {
- if (distsRight[i].dist == lastRight) {
- it = seen.find(db[distsRight[i].index]->getName());
-
- if (it == seen.end()) {
-// cout << "newLoop-right\t" << db[distsRight[i].index]->getName() << '\t' << distsRight[i].dist << endl;
- dists.push_back(distsRight[i]);
- seen[db[distsRight[i].index]->getName()] = db[distsRight[i].index]->getName();
-// numWanted++;
- }
- }
- else { break; }
- i++;
- }
-*/
- numWanted = dists.size();
-
- if (numWanted > dists.size()) {
- //m->mothurOut("numwanted is larger than the number of template sequences, adjusting numwanted."); m->mothurOutEndLine();
- numWanted = dists.size();
- }
+ //numWanted = dists.size();
-//cout << numWanted << endl;
- for (int i = 0; i < numWanted; i++) {
+ //cout << numWanted << endl;
+ for (int i = 0; i < dists.size(); i++) {
// cout << db[dists[i].index]->getName() << '\t' << dists[i].dist << endl;
- if (db[dists[i].index]->getName() != querySeq->getName()) {
- Sequence* temp = new Sequence(db[dists[i].index]->getName(), db[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
+ if (thisTemplate[dists[i].index]->getName() != querySeq->getName()) {
+ Sequence* temp = new Sequence(thisTemplate[dists[i].index]->getName(), thisTemplate[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
seqsMatches.push_back(temp);
- indexes.push_back(dists[i].index);
}
}
DeCalculator() { m = MothurOut::getInstance(); }
~DeCalculator() {};
- vector<Sequence*> findClosest(Sequence*, vector<Sequence*>, int&, vector<int>&); //takes querySeq, a reference db, numWanted and indexes
+ vector<Sequence*> findClosest(Sequence*, vector<Sequence*>&, vector<Sequence*>&, int&); //takes querySeq, a reference db, filteredRefDB, numWanted
Sequence* findClosest(Sequence*, vector<Sequence*>);
set<int> getPos() { return h; }
void setMask(string);
*/
#include "maligner.h"
-#include "kmerdb.hpp"
-#include "blastdb.hpp"
-/***********************************************************************/
-Maligner::Maligner(vector<Sequence*> temp, int num, int match, int misMatch, float div, int ms, int minCov, string mode, Database* dataLeft, Database* dataRight) :
- db(temp), numWanted(num), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov), searchMethod(mode), databaseLeft(dataLeft), databaseRight(dataRight) {
-
+/***********************************************************************/ //int num, int match, int misMatch, , string mode, Database* dataLeft, Database* dataRight
+Maligner::Maligner(vector<Sequence*> temp, int match, int misMatch, float div, int ms, int minCov) : db(temp), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov) {
+ //numWanted(num), , searchMethod(mode), databaseLeft(dataLeft), databaseRight(dataRight)
m = MothurOut::getInstance();
-// cout << matchScore << '\t' << misMatchPenalty << endl;
-//
-// matchScore = 1;
-// misMatchPenalty = -1;
-
- }
-
+}
/***********************************************************************/
string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
try {
string chimera;
- if (searchMethod == "distance") {
- //find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate
- refSeqs = decalc->findClosest(query, db, numWanted, indexes);
- }else if (searchMethod == "blast") {
- refSeqs = getBlastSeqs(query, numWanted); //fills indexes
- }else if (searchMethod == "kmer") {
- refSeqs = getKmerSeqs(query, numWanted); //fills indexes
- }else { m->mothurOut("not valid search."); exit(1); } //should never get here
-
- if (m->control_pressed) { return chimera; }
+ //copy refSeqs so that filter does not effect original
+ for(int i = 0; i < db.size(); i++) {
+ Sequence* newSeq = new Sequence(db[i]->getName(), db[i]->getAligned());
+ refSeqs.push_back(newSeq);
+ }
refSeqs = minCoverageFilter(refSeqs);
-
-
if (refSeqs.size() < 2) {
for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
percentIdenticalQueryChimera = 0.0;
}
int chimeraPenalty = computeChimeraPenalty();
- //cout << "chimeraPenalty = " << chimeraPenalty << endl;
+
//fills outputResults
chimera = chimeraMaligner(chimeraPenalty, decalc);
results temp;
temp.parent = refSeqs[seqIndex]->getName();
- temp.parentAligned = db[indexes[seqIndex]]->getAligned();
+ temp.parentAligned = db[seqIndex]->getAligned();
temp.nastRegionStart = spotMap[regionStart];
temp.nastRegionEnd = spotMap[regionEnd];
temp.regionStart = regionStart;
parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart+1));
temp.queryToParentLocal = computePercentID(queryInRegion, parentInRegion);
-
+
+ //cout << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << endl;
outputResults.push_back(temp);
}
}
}
//***************************************************************************************************************
-vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
- try {
- indexes.clear();
- vector<Sequence*> refResults;
-
- //get parts of query
- string queryUnAligned = q->getUnaligned();
- string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
- string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
-
- Sequence* queryLeft = new Sequence(q->getName()+"left", leftQuery);
- Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
-
- vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
- vector<float> leftScores = databaseLeft->getSearchScores();
- vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
- vector<float> rightScores = databaseLeft->getSearchScores();
-
- //if ((tempIndexesRight.size() == 0) && (tempIndexesLeft.size() == 0)) { m->mothurOut("megablast returned " + toString(tempIndexesRight.size()) + " results for the right end, and " + toString(tempIndexesLeft.size()) + " for the left end. Needed " + toString(num+1) + ". Unable to process sequence " + q->getName()); m->mothurOutEndLine(); return refResults; }
-
- vector<int> smaller;
- vector<float> smallerScores;
- vector<int> larger;
- vector<float> largerScores;
-
- if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight; smallerScores = rightScores; larger = tempIndexesLeft; largerScores = leftScores; }
- else { smaller = tempIndexesLeft; smallerScores = leftScores; larger = tempIndexesRight; largerScores = rightScores; }
-
- //for (int i = 0; i < smaller.size(); i++) { cout << "smaller = " << smaller[i] << '\t' << smallerScores[i] << endl; }
- //cout << endl;
- //for (int i = 0; i < larger.size(); i++) { cout << "larger = " << larger[i] << '\t' << largerScores[i] << endl; }
-
- //merge results
- map<int, int> seen;
- map<int, int>::iterator it;
- float lastSmaller = smallerScores[0];
- float lastLarger = largerScores[0];
- int lasti = 0;
- vector<int> mergedResults;
- for (int i = 0; i < smaller.size(); i++) {
- //add left if you havent already
- it = seen.find(smaller[i]);
- if (it == seen.end()) {
- mergedResults.push_back(smaller[i]);
- seen[smaller[i]] = smaller[i];
- lastSmaller = smallerScores[i];
- }
-
- //add right if you havent already
- it = seen.find(larger[i]);
- if (it == seen.end()) {
- mergedResults.push_back(larger[i]);
- seen[larger[i]] = larger[i];
- lastLarger = largerScores[i];
- }
-
- lasti = i;
- //if (mergedResults.size() > num) { break; }
- }
-
- //save lasti for smaller ties below
- /*lasti++;
- int iSmaller = lasti;
-
- if (!(mergedResults.size() > num)) { //if we still need more results.
- for (int i = smaller.size(); i < larger.size(); i++) {
- it = seen.find(larger[i]);
- if (it == seen.end()) {
- mergedResults.push_back(larger[i]);
- seen[larger[i]] = larger[i];
- lastLarger = largerScores[i];
- }
-
- lasti = i;
- if (mergedResults.size() > num) { break; }
- }
- }
-
-
- //add in any ties from smaller
- while (iSmaller < smaller.size()) {
- if (smallerScores[iSmaller] == lastSmaller) {
- it = seen.find(smaller[iSmaller]);
-
- if (it == seen.end()) {
- mergedResults.push_back(smaller[iSmaller]);
- seen[smaller[iSmaller]] = smaller[iSmaller];
- }
- }
- else { break; }
- iSmaller++;
- }
-
- lasti++;
- //add in any ties from larger
- while (lasti < larger.size()) {
- if (largerScores[lasti] == lastLarger) { //is it a tie
- it = seen.find(larger[lasti]);
-
- if (it == seen.end()) { //we haven't already seen it
- mergedResults.push_back(larger[lasti]);
- seen[larger[lasti]] = larger[lasti];
- }
- }
- else { break; }
- lasti++;
- }
- */
-
- for (int i = smaller.size(); i < larger.size(); i++) {
- //add right if you havent already
- it = seen.find(larger[i]);
- if (it == seen.end()) {
- mergedResults.push_back(larger[i]);
- seen[larger[i]] = larger[i];
- lastLarger = largerScores[i];
- }
- }
- numWanted = mergedResults.size();
-
- if (mergedResults.size() < numWanted) { numWanted = mergedResults.size(); }
-//cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted << endl;
- for (int i = 0; i < numWanted; i++) {
-//cout << db[mergedResults[i]]->getName() << '\t' << mergedResults[i] << endl;
-
- if (db[mergedResults[i]]->getName() != q->getName()) {
- Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
- refResults.push_back(temp);
- indexes.push_back(mergedResults[i]);
- //cout << db[mergedResults[i]]->getName() << endl;
- }
-
-//cout << mergedResults[i] << endl;
- }
-//cout << "done " << q->getName() << endl;
- delete queryRight;
- delete queryLeft;
-
- return refResults;
- }
- catch(exception& e) {
- m->errorOut(e, "Maligner", "getBlastSeqs");
- exit(1);
- }
-}
-//***************************************************************************************************************
-vector<Sequence*> Maligner::getKmerSeqs(Sequence* q, int num) {
- try {
- indexes.clear();
-
- //get parts of query
- string queryUnAligned = q->getUnaligned();
- string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
- string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
-
- Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
- Sequence* queryRight = new Sequence(q->getName(), rightQuery);
-
- vector<int> tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, numWanted);
- vector<int> tempIndexesRight = databaseRight->findClosestSequences(queryRight, numWanted);
- vector<float> scoresLeft = databaseLeft->getSearchScores();
- vector<float> scoresRight = databaseRight->getSearchScores();
-
- //merge results
- map<int, int> seen;
- map<int, int>::iterator it;
- float lastRight = scoresRight[0];
- float lastLeft = scoresLeft[0];
- //int lasti = 0;
- vector<int> mergedResults;
- for (int i = 0; i < tempIndexesLeft.size(); i++) {
- //add left if you havent already
- it = seen.find(tempIndexesLeft[i]);
- if (it == seen.end()) {
- mergedResults.push_back(tempIndexesLeft[i]);
- seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
- lastLeft = scoresLeft[i];
- }
-
- //add right if you havent already
- it = seen.find(tempIndexesRight[i]);
- if (it == seen.end()) {
- mergedResults.push_back(tempIndexesRight[i]);
- seen[tempIndexesRight[i]] = tempIndexesRight[i];
- lastRight = scoresRight[i];
- }
-
- //if (mergedResults.size() > numWanted) { lasti = i; break; } //you have enough results
- }
-
- //add in sequences with same distance as last sequence added
- /*lasti++;
- int i = lasti;
- while (i < tempIndexesLeft.size()) {
- if (scoresLeft[i] == lastLeft) {
- it = seen.find(tempIndexesLeft[i]);
-
- if (it == seen.end()) {
- mergedResults.push_back(tempIndexesLeft[i]);
- seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
- }
- }
- else { break; }
- i++;
- }
-
- // cout << "lastRight\t" << lastRight << endl;
- //add in sequences with same distance as last sequence added
- i = lasti;
- while (i < tempIndexesRight.size()) {
- if (scoresRight[i] == lastRight) {
- it = seen.find(tempIndexesRight[i]);
-
- if (it == seen.end()) {
- mergedResults.push_back(tempIndexesRight[i]);
- seen[tempIndexesRight[i]] = tempIndexesRight[i];
- }
- }
- else { break; }
- i++;
- }*/
-
- numWanted = mergedResults.size();
-
- if (numWanted > mergedResults.size()) {
- //m->mothurOut("numwanted is larger than the number of template sequences, adjusting numwanted."); m->mothurOutEndLine();
- numWanted = mergedResults.size();
- }
-
-
-//cout << q->getName() << endl;
- vector<Sequence*> refResults;
- for (int i = 0; i < numWanted; i++) {
-//cout << db[mergedResults[i]]->getName() << endl;
- if (db[mergedResults[i]]->getName() != q->getName()) {
- Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
- refResults.push_back(temp);
- indexes.push_back(mergedResults[i]);
- }
- }
-//cout << endl;
- delete queryRight;
- delete queryLeft;
-
- return refResults;
- }
- catch(exception& e) {
- m->errorOut(e, "Maligner", "getKmerSeqs");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
public:
- Maligner(vector<Sequence*>, int, int, int, float, int, int, string, Database*, Database*);
+ Maligner(vector<Sequence*>, int, int, float, int, int); //int, int, int, , string, Database*, Database*
~Maligner() {};
string getResults(Sequence*, DeCalculator*);
Sequence* query;
vector<Sequence*> refSeqs;
vector<Sequence*> db;
- int numWanted, matchScore, misMatchPenalty, minCoverage, minSimilarity;
- string searchMethod;
+ int minCoverage, minSimilarity, matchScore, misMatchPenalty;
float minDivR, percentIdenticalQueryChimera;
vector<results> outputResults;
- vector<int> indexes; //stores index into template seqs of the refSeqs, so we can return the whole sequence rather than the trimmed and filtered one
map<int, int> spotMap;
- Database* databaseLeft;
- Database* databaseRight;
vector<Sequence*> minCoverageFilter(vector<Sequence*>); //removes top matches that do not have minimum coverage with query.
int computeChimeraPenalty();
string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence*>);
float computePercentID(string, string);
string chimeraMaligner(int, DeCalculator*);
- vector<Sequence*> getBlastSeqs(Sequence*, int);
- vector<Sequence*> getKmerSeqs(Sequence*, int);
MothurOut* m;
};
#include "slayer.h"
/***********************************************************************/
-Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp) :
- windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
+Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp, int mi) :
+ minBS(mi), windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
/***********************************************************************/
string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
try {
vector<data_struct> all; all.clear();
+ myQuery = *query;
+ /*cout << "here" << endl;
+ query->setName("S000381746"); query->setAligned("...............................................................................................................................................A-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-G-CG----------G-CAG-CG-G---------------------------GA-GG-A-AG----------------------------------------------------CTT-G----------------------------------------------------------------------------------CTT-CCTC----------------G-CC--G--GC--G--AG-C-GG-C-GG-A--C-------------GGG-TGAGT-A--AT-GT-C-T-G-GG---G-A--T-CT-G--C-C-CGA--TG-G------------------------------------------------------------------A-GG----GGG-AT-AA-CCA-------------------------C-T-G-----------------------GAA-A---CGG-TGG-CTAA-TA---CC-G--C-AT-A----------A--------------------C-------------------------------------GT-C-----------------------------------------------------------------------------------------------------------------------G-CA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAA--G-T-G-GG-----G--GA-C--C--------------------------------------------------------------------------------------------------------------------TTC-G----------------------------------------------------------------------------------------------------------------------G-G--CC-TC--A---C-A--------------C----C-A---T-CG-G---AT---G-A-----A-CCC-AGA--T-GGG--A------TT--A--G-CT-A----G---TAGG-T-G-GG-G-T----AAT-GG-C-T-C-ACCT--A-GG-C-G--A-CG-A------------TCC-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AT--G-AC-C-AG-CCAC-A-CTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GC-GC-A----A-G-CC-T-GA-TG-CA-GCCA-TGCC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TC-A-G--C-GAG----GA-G--G---AA-GGTG---GTGA-GC----T--T--AA-T---A----------CG-CTCAT-CAA-TT-GA-CG-TT-A-C-TC-G-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGC-AC--G-CA-G-G-C-G------------G--T-TT-G-T-T-AA----G-T-C-A---G-ATG-TG-A-AA-TC--CC-CGA-G--------------------------------------------------------------------CT-T-AA-------------------------------------------------------------------------CT-T-G-GG-AA-C----T-G-C-A-T-T--------T--GA-A-A-C-T-G-GCA--A-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-A-G-A-G-T-C-----T-CG--TA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-T-GGA--GG-A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-CCCTG------G-AC-GA--------------------------------------------------------------AG-A-C-T--GA--CG-----CT-CA-GG--T-G-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CCG-T-AAA--C-GATG-TC--GA-TT---------T-GG--A--G-G-TT-G-TG-C--C--------------------------------------------------------------------------------------CTT-GA--------------------------------------------------------------------------------------------------------------------------------------------------G-G-C-GT--G-G-C-T-TC-C------GG--A----GC-TAA--CG-C-G-T--T--AA-AT--C----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------TGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-TACTC-TT-G-AC-A-T-C--------------CAG-A-G-------------A-AC-T-T-T--CC--A-GA-G-A-T--G-G-A--T-T-G-G--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG----A----A---CT-CTG---A--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TT-G--TGA-AA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TC--C-TTTG--T-T-G-C-C---AG-C-G--G--T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----C----C-G------------G----G---A-A--CT---------------C-A-A-A-G-GA-G--AC-T-G-CCA--G-T------------------------------------G-A---TAA----------------------------------A-C-T-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AC-G--AG-T-A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGTA-T-A--C-AAA-GA-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--ACCT-G-C--G---------------------------------------A-GG-G-C-----------A--A-G-CG---G----------A--CCT-C------A-T-AAAGT-AC-G-T-C-G-TAG-TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-ACTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-T----AGA-TC-A-G--A------AT--GCT-AC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-GC-AAA--A-GAA------G--T-AGG-TA-G-C-T-T-AA-C-C-------------------------------------------------------------T-TC-G------------------------------------------------------------------------------------------------------GG-A--GG-G--C---GC-TTA--CC--ACT-T----T-GT..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................");
+ refSeqs.resize(2);
+ refSeqs[1]->setName("S000381740"); refSeqs[1]->setAligned("...............................................................................................................................................a-c-gc--tgg-c--g-gc-a-gg--c----c-t--aacaca-t-gc-a-agt-cga-g-cg----------g-tag-ca-c----------------------------agga-g-ag----------------------------------------------------ctt-g----------------------------------------------------------------------------------ctc-tctg----------------g-gt--g--ac--g--ag-c-gg-c-gg-a--c-------------ggg-tgagt-a--at-gt-c-t-g-gg---a-a--a-ct-g--c-c-tga--tg-g------------------------------------------------------------------a-gg----ggg-at-aa-cta-------------------------c-t-g-----------------------gaa-a---cgg-tag-ctaa-ta---cc-g--c-at-a----------a--------------------c-------------------------------------gt-c-----------------------------------------------------------------------------------------------------------------------t-ac-g--------------------------------------------------------------------------------------------------------------------------------------g-a-c---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------caaa--g-t-g-gg-----g--ga-c--c--------------------------------------------------------------------------------------------------------------------ttc-g----------------------------------------------------------------------------------------------------------------------g-g--cc-tc--a---c-g--------------c----c-a---t-ca-g---at---g-t-----g-ccc-aga--t-ggg--a------tt--a--g-ct-a----g---tagg-t-g-gg-g-t----aat-gg-c-t-c-acct--a-gg-c-g--a-cg-a------------tcc-c-t------ag-ct-g-g-tct-g-ag----a--gg-at--g-ac-c-ag-ccac-a-ctgga--a-c-tg-a-ga-c-ac-g-g-tccaga-ctcc-tac-g--g-g-a-g-gc-a-gc-a-g-tg---gg-g-a-ata-ttgca-c-aa-t-gg--gc-gc-a----a-g-cc-t-ga-tg-ca-gcca-tgcc-g-cg-t---g-t-g--t--ga-a-g--a--a-g-g-cc-----tt-cg---------g-g-t-t-g-t--a---aa-g-cac--------tt-tc-a-g--c-gag----ga-g--g---aa-gggc---gatg-tc----t--t--aa-t---a----c-----gg-c-agc-gca-tt-ga-cg-tt-a-c-tc-g-ca-g---------aa-----------gaagc-acc-gg-c-taa---c--t-ccgt--gcca--g-c---a--gccg---c-gg--ta-at--ac---gg-ag-ggt-gca-a-g-cg-ttaa-t-cgg-aa-tt-a--c-t--gggc-gta----aa-gcgc-ac--g-ca-g-g-c-g------------g--t-tt-g-t-t-aa----g-t-c-a---g-atg-tg-a-aa-tc--cc-cgc-g--------------------------------------------------------------------ct-t-aa-------------------------------------------------------------------------cg-t-g-gg-aa-c----t-g-c-a-t-t--------t--ga-a-a-c-t-g-gca--a-g-c---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------t-a-g-a-g-t-c-----t-cg--ta-g-a------------g-gg-g-gg-t----ag--aatt-cca-g-gt--gt-a-gcg-gtgaaa-tg-cgt-agag-a-tc-t-gga--gg-a-at-a-cc-gg--t--g--gc-gaa-g--g-c---g----g--c-c-ccctg------g-ac-ga--------------------------------------------------------------ag-a-c-t--ga--cg-----ct-ca-gg--t-g-cga--aa-g-c--------------g-tggg-gag-c-a-aaca--gg-atta-g-ata-c-----cc-t-g-gta-g-t----c-ca--c-g-ctg-t-aaa--c-gatg-tc--ga-tt---------t-gg--a--g-g-tt-g-tg-c--c--------------------------------------------------------------------------------------ctt-ga--------------------------------------------------------------------------------------------------------------------------------------------------g-g-c-gt--g-g-c-t-tc-c------gg--a----gc-taa--cg-c-g-t--t--aa-at--c----g-acc-gcc-t-g-gg-gag-ta---cgg-----c-c--g-c-a-a-ggt-t--aaa-actc-aaa---------tgaa-ttg-acggg-g-g-cccg----c-a--c-a-a-gcg-gt-g--g--ag-ca-t--gt-ggt-tt-aatt-c-g-atg-caac-g-cg-a-ag-a-a-cc-tt-a-cc-tactc-tt-g-ac-a-t-c--------------cag-a-g-------------a-ac-t-t-t--cc--a-ga-g-a-t--g-g-a--t-t-g-g--t-g-----cc-------------------------------------t--tc-g------------------------------------------gg----a----a---ct-ctg---a--ga---------------------------------------------------c-a-g-g-t-gctg-ca-tgg-ct--gtc-gtc-a-gc-tc---g-tg-tt-g--tga-aa-tgt-t-gg-g-tt-aa-gt-cccgc-aa--------c-gag-cgc-a-acc-c-t-ta--tc--c-tttg--t-t-g-c-c---ag-c-g--a--t-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tcg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------g----t----c-g------------g----g---a-a--ct---------------c-a-a-a-g-ga-g--ac-t-g-ccg--g-t------------------------------------g-a---taa----------------------------------a-c-c-g--g-a-gg-a--agg-t--gggg-a-tgac-gtc--aagt-c---atc-a-t-g-g-c-c-ctt----ac-g--ag-t-a-gg-gc-ta-cac-acgtg-c--ta--caatg---g-cgta-t-a--c-aaa-ga-ga--------------------------------------------------------------------------------------------------a-g-c-g-a--a-ctcg-c--g---------------------------------------a-ga-g-c-----------a--a-g-cg---g----------a--cct-c------a-t-aaagt-ac-g-t-c-g-tag-tcc--------gga-t-tggag-tc--t-gcaa-ct-c-------------------------------------------------------------------------------------------------g-actcc-a-t-g-aa-g-tc-ggaat-cg-c-ta--g-ta-at-c-g-t----aga-tc-a-g--a------at--gct-ac-g-gt-g-aat-acgt-t-cccgggcct-tgta----cacaccg-ccc-gtc-----a---ca--cca-tg-gg-a--g---tgg-g-tt-gc-aaa--a-gaa------g--t-agg-ta-g-c-t-t-aa-c-c-------------------------------------------------------------t-tc-g------------------------------------------------------------------------------------------------------gg-a--gg-g--c---gc-tta--cc--act-t----t-gtg-at-tca------------------------t.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................");
+ refSeqs[0]->setName("7000004131500404"); refSeqs[0]->setAligned(".........................................................................................................................................AT-TGAA-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-G-CG----------G-CAG-CG-G----------------------------AAAG-A-AG----------------------------------------------------CTT-G---------------------------------------------------------------------------------ACTT-CTTT----------------G-CC--G--GC--G--AG-C-GG-C-GG-A--C-------------GGG-TGAGT-A--AT-GT-C-T-G-GG---G-A--T-CT-G--C-C-CGA--TG-G------------------------------------------------------------------A-GG----GGG-AT-AA-CTA-------------------------C-T-G-----------------------GAA-A---CGG-TAG-CTAA-TA---CC-G--C-AT-A----------A--------------------C-------------------------------------GT-C-----------------------------------------------------------------------------------------------------------------------G-CA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAA--G-T-G-GG-----G--GA-C--C--------------------------------------------------------------------------------------------------------------------TTC-G----------------------------------------------------------------------------------------------------------------------G-G--CC-TC--A---C-A--------------C----C-A---T-CG-G---AT---G-A-----A-CCC-AGA--T-GGG--A------TT--A--G-CT-A----G---TAGG-T-G-GG-G-T----AAT-GG-C-T-C-ACCT--A-GG-C-G--A-CG-A------------TCC-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AT--G-AC-C-AG-CCAC-A-CTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GG-GA-A----A-C-CC-T-GA-TG-CA-GCCA-TGCC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TC-A-G--C-GGG----GA-A--G---AA-GGCG---TT-A-GC---GT--T--AA-C---A----G-----CG-C-TAT-CGA-TT-GA-CG-TT-A-C-CT-G-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGT-AC--G-CA-G-G-C-G------------G--T-CT-G-T-T-AA----G-T-C-A---G-ATG-TG-A-AA-TC--CC-CGG-G--------------------------------------------------------------------CT-T-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-T--------T--GA-A-A-C-T-G-GCA--G-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-A-G-A-G-T-C-----T-CG--TA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-T-GGA--GG-A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-CCCTG------G-AC-GA--------------------------------------------------------------AG-A-C-T--GA--CG-----CT-CA-GG--T-A-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CTG-T-AAA--C-GATG-TC--GA-TT---------T-GA--A--G-G-TT-G-TG-G--C--------------------------------------------------------------------------------------CTT-GA--------------------------------------------------------------------------------------------------------------------------------------------------G-C-T-GT--G-G-C-T-TT-C------GG--A----GC-TAA--CG-C-G-T--T--AA-AT--C----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------TGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-TACTC-TT-G-AC-A-T-C--------------CAG-A-G-------------A-AC-T-T-G--GC--A-GA-G-A-T--G-C-C--T-T-G-G--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG----A----G---CT-CTG---A--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TT-G--TGA-AA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TC--C-TTTG--T-T-G-C-C---AG-C-G--A--T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----T----C-G------------G----G---A-A--CT---------------C-A-A-A-G-GA-G--AC-T-G-CCG--G-T------------------------------------G-A---TAA----------------------------------A-C-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AC-G--AG-T-A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGCA-T-A--C-AAA-GA-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--T-CTCG-C--G---------------------------------------A-GA-G-T-----------C--A-G-CG---G----------A--CCT-C------A-C-AAAGT-GC-G-T-C-G-TAG-TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-ACTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-T----GGA-TC-A-G--A------AT--GCC-AC-G-GT-G-AAT-ACGT-T-CCTGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-GC-AAA--A-GAA------G--T-AGG-TA-G-C-T-T-AA-C-C-------------------------------------------------------------T-TC-G------------------------------------------------------------------------------------------------------GG-A--GG-G--C---GC-TTA--CC--ACT-T----T-GTG-AT-TCA------------------------TG--ACT-GGGG-TG-AAG-TCGTAACAA-GGTAA-CCGT-AGGGGAA-CCT......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................");
+ for (int i = 0; i < refSeqs.size(); i++) {
+ string newAligned = "";
+ for (int j = 0; j < refSeqs[i]->getAligned().length(); j++) {
+ newAligned += toupper(refSeqs[i]->getAligned()[j]);
+ }
+ refSeqs[i]->setAligned(newAligned);
+ }*/
for (int i = 0; i < refSeqs.size(); i++) {
map<int, int> spots; //map from spot in original sequence to spot in filtered sequence for query and both parents
vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
-
+ //cout << divs.size() << endl;
if (m->control_pressed) {
delete q;
delete leftParent;
//if (abs(logR) < 1 ) {
float BS_A, BS_B;
- bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B);
+ bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters);
if (m->control_pressed) {
delete q;
}
}
/***********************************************************************/
-int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB) {
+int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB, int numIters) {
try {
srand((unsigned)time( NULL ));
int numLeft = max(1, int(left.size() * percentSNPSample/(float)100 + 0.5));
int numRight = max(1, int(right.size() * percentSNPSample/(float)100 + 0.5));
- for (int i = 0; i < iters; i++) {
+ for (int i = 0; i < numIters; i++) {
//random sampling with replacement.
if (m->control_pressed) { return 0; }
BSA = (float) count_A / (float) iters * 100;
BSB = (float) count_B / (float) iters * 100;
//cout << "bsa = " << BSA << " bsb = " << BSB << endl;
+
+ //run borderline bootstrap values longer
+ //if (numIters < 1000) {
+ //are you within 10 points of min bootstrap value cutoff
+ // if (((abs((double)(BSA - minBS))) <= 5) || ((abs((double)(BSB - minBS))) <= 5)) {
+ // m->mothurOut("extending bootstrap for " + myQuery.getName()); m->mothurOutEndLine();
+ // bootstrapSNPS(left, right, BSA, BSB, 1000);
+ // }
+ //}
return 0;
public:
- Slayer(int, int, int, float, int, int);
+ Slayer(int, int, int, float, int, int, int);
~Slayer() {};
string getResults(Sequence*, vector<Sequence*>);
private:
- int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample;
+ int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample, minBS;
float divRThreshold;
vector<data_struct> outputResults;
vector< map<int, int> > baseSpots;
+ Sequence myQuery;
map<int, int> verticalFilter(vector<Sequence*>);
float computePercentID(string, string, int, int);
vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*, map<int, int>&);
vector<snps> getSNPS(string, string, string, int, int);
- int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&);
+ int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&, int);
float snpQA(vector<snps>);
float snpQB(vector<snps>);
float snpAB(vector<snps>);
projects / mothur.git / commitdiff