#include "maligner.h"
+/***********************************************************************/ //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();
+
+}
/***********************************************************************/
-Maligner::Maligner(vector<Sequence*> temp, int num, int match, int misMatch, float div, int minCov) :
- db(temp), numWanted(num), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minCoverage(minCov) {}
-/***********************************************************************/
-string Maligner::getResults(Sequence* q) {
+string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
try {
+ outputResults.clear();
+
//make copy so trimming doesn't destroy query from calling class - remember to deallocate
query = new Sequence(q->getName(), q->getAligned());
string chimera;
-
- decalc = new DeCalculator();
-
- //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);
- ofstream out;
- string outFile = "parentsOf" + query->getName();
- openOutputFile(outFile, out);
- for (int i = 0; i < refSeqs.size(); i++) { refSeqs[i]->printSequence(out); }
- out.close();
+ //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);
}
int chimeraPenalty = computeChimeraPenalty();
-
+
+ //fills outputResults
+ chimera = chimeraMaligner(chimeraPenalty, decalc);
+
+ if (m->control_pressed) { return chimera; }
+
+ //free memory
+ delete query;
+
+ for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
+
+ return chimera;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "getResults");
+ exit(1);
+ }
+}
+/***********************************************************************/
+string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
+ try {
+
+ string chimera;
+
//trims seqs to first non gap char in all seqs and last non gap char in all seqs
- decalc->trimSeqs(query, refSeqs);
+ spotMap = decalc->trimSeqs(query, refSeqs);
+ //you trimmed the whole sequence, skip
+ if (query->getAligned() == "") { return "no"; }
+
vector<Sequence*> temp = refSeqs;
temp.push_back(query);
-
+
verticalFilter(temp);
+
+ //for (int i = 0; i < refSeqs.size(); i++) { cout << refSeqs[i]->getName() << endl << refSeqs[i]->getAligned() << endl; }
vector< vector<score_struct> > matrix = buildScoreMatrix(query->getAligned().length(), refSeqs.size()); //builds and initializes
- fillScoreMatrix(matrix, refSeqs, chimeraPenalty);
-
- vector<score_struct> path = extractHighestPath(matrix);
+ if (m->control_pressed) { return chimera; }
- vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
+ fillScoreMatrix(matrix, refSeqs, chimeraPenalty);
+
+ vector<trace_struct> trace = extractHighestPath(matrix);
+
+ //cout << "traces\n";
+ //for(int i=0;i<trace.size();i++){
+ // cout << trace[i].col << '\t' << trace[i].oldCol << '\t' << refSeqs[trace[i].row]->getName() << endl;
+ //}
if (trace.size() > 1) { chimera = "yes"; }
- else { chimera = "no"; }
-
- int traceStart = path[0].col;
- int traceEnd = path[path.size()-1].col;
+ else { chimera = "no"; return chimera; }
+ int traceStart = trace[0].col;
+ int traceEnd = trace[trace.size()-1].oldCol;
string queryInRange = query->getAligned();
- queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
-
- string chimeraSeq = constructChimericSeq(trace, refSeqs);
+ queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));
- percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
-
- delete decalc;
+ if (m->control_pressed) { return chimera; }
//save output results
for (int i = 0; i < trace.size(); i++) {
results temp;
temp.parent = refSeqs[seqIndex]->getName();
+ temp.parentAligned = db[seqIndex]->getAligned();
+ temp.nastRegionStart = spotMap[regionStart];
+ temp.nastRegionEnd = spotMap[regionEnd];
temp.regionStart = regionStart;
temp.regionEnd = regionEnd;
string parentInRange = refSeqs[seqIndex]->getAligned();
- parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart+1));
+ parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart));
temp.queryToParent = computePercentID(queryInRange, parentInRange);
temp.divR = (percentIdenticalQueryChimera / temp.queryToParent);
-
+
string queryInRegion = query->getAligned();
- queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart+1));
+ queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart));
string parentInRegion = refSeqs[seqIndex]->getAligned();
- parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart+1));
+ parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart));
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);
}
- //free memory
- delete query;
- for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; }
-
return chimera;
}
catch(exception& e) {
- errorOut(e, "Maligner", "getResults");
+ m->errorOut(e, "Maligner", "chimeraMaligner");
exit(1);
}
}
//if coverage above minimum
if (coverage > minCoverage) {
newRefs.push_back(ref[i]);
+ }else {
+ delete ref[i];
}
}
return newRefs;
}
catch(exception& e) {
- errorOut(e, "Maligner", "minCoverageFilter");
+ m->errorOut(e, "Maligner", "minCoverageFilter");
exit(1);
}
}
try {
int numAllowable = ((1.0 - (1.0/minDivR)) * query->getNumBases());
-
+
+// if(numAllowable < 1){ numAllowable = 1; }
+
int penalty = int(numAllowable + 1) * misMatchPenalty;
-
+
return penalty;
}
catch(exception& e) {
- errorOut(e, "Maligner", "computeChimeraPenalty");
+ m->errorOut(e, "Maligner", "computeChimeraPenalty");
exit(1);
}
}
if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; }
}
+ map<int, int> newMap;
//for each sequence
for (int i = 0; i < seqs.size(); i++) {
string seqAligned = seqs[i]->getAligned();
string newAligned = "";
+ int count = 0;
for (int j = 0; j < seqAligned.length(); j++) {
//if this spot is not a gap
- if (filterString[j] == '1') { newAligned += seqAligned[j]; }
+ if (filterString[j] == '1') {
+ newAligned += seqAligned[j];
+ newMap[count] = spotMap[j];
+ count++;
+ }
}
seqs[i]->setAligned(newAligned);
}
-
+ spotMap = newMap;
}
catch(exception& e) {
- errorOut(e, "Maligner", "verticalFilter");
+ m->errorOut(e, "Maligner", "verticalFilter");
exit(1);
}
}
vector< vector<score_struct> > Maligner::buildScoreMatrix(int cols, int rows) {
try{
- vector< vector<score_struct> > m; m.resize(rows);
+ vector< vector<score_struct> > m(rows);
- for (int i = 0; i < m.size(); i++) {
+ for (int i = 0; i < rows; i++) {
for (int j = 0; j < cols; j++) {
//initialize each cell
return m;
}
catch(exception& e) {
- errorOut(e, "Maligner", "buildScoreMatrix");
+ m->errorOut(e, "Maligner", "buildScoreMatrix");
exit(1);
}
}
+
//***************************************************************************************************************
-void Maligner::fillScoreMatrix(vector<vector<score_struct> >& m, vector<Sequence*> seqs, int penalty) {
+
+void Maligner::fillScoreMatrix(vector<vector<score_struct> >& ms, vector<Sequence*> seqs, int penalty) {
try{
//get matrix dimensions
//are you both gaps?
if ((!isalpha(queryAligned[0])) && (!isalpha(subjectAligned[0]))) {
- m[i][0].score = 0;
- }else if (queryAligned[0] == subjectAligned[0]) {
- m[i][0].score = matchScore;
+ ms[i][0].score = 0;
+// ms[i][0].mismatches = 0;
+ }else if (queryAligned[0] == subjectAligned[0]) { //|| subjectAligned[0] == 'N')
+ ms[i][0].score = matchScore;
+// ms[i][0].mismatches = 0;
}else{
- m[i][0].score = 0;
+ ms[i][0].score = 0;
+// ms[i][0].mismatches = 1;
}
}
if ((!isalpha(queryAligned[j])) && (!isalpha(subjectAligned[j]))) {
//leave the same
}else if ((toupper(queryAligned[j]) == 'N') || (toupper(subjectAligned[j]) == 'N')) {
+ //matchMisMatchScore = matchScore;
//leave the same
}else if (queryAligned[j] == subjectAligned[j]) {
matchMisMatchScore = matchScore;
+// ms[i][j].mismatches = ms[i][j-1].mismatches;
}else if (queryAligned[j] != subjectAligned[j]) {
matchMisMatchScore = misMatchPenalty;
+// ms[i][j].mismatches = ms[i][j-1].mismatches + 1;
}
//compute score based on previous columns scores
for (int prevIndex = 0; prevIndex < numRows; prevIndex++) { //iterate through rows
- int sumScore = matchMisMatchScore + m[prevIndex][j-1].score;
+ int sumScore = matchMisMatchScore + ms[prevIndex][j-1].score;
//you are not at yourself
if (prevIndex != i) { sumScore += penalty; }
if (sumScore < 0) { sumScore = 0; }
- if (sumScore > m[i][j].score) {
- m[i][j].score = sumScore;
- m[i][j].prev = prevIndex;
+ if (sumScore > ms[i][j].score) {
+ ms[i][j].score = sumScore;
+ ms[i][j].prev = prevIndex;
}
}
}
}
+ /* for(int i=0;i<numRows;i++){
+ cout << seqs[i]->getName();
+ for(int j=0;j<numCols;j++){
+ cout << '\t' << ms[i][j].mismatches;
+ }
+ cout << endl;
+ }
+ cout << endl;*/
+ /*cout << numRows << '\t' << numCols << endl;
+ for(int i=0;i<numRows;i++){
+ cout << seqs[i]->getName() << endl << seqs[i]->getAligned() << endl << endl;
+ if ((seqs[i]->getName() == "S000003470") || (seqs[i]->getName() == "S000383265") || (seqs[i]->getName() == "7000004128191054")) {
+ for(int j=0;j<numCols;j++){
+ cout << '\t' << ms[i][j].score;
+ }
+ cout << endl;
+ }
+ }
+ cout << endl;*/
+ /*for(int i=0;i<numRows;i++){
+ cout << seqs[i]->getName();
+ for(int j=0;j<numCols;j++){
+ cout << '\t' << ms[i][j].prev;
+ }
+ cout << endl;
+ }*/
+
+
}
catch(exception& e) {
- errorOut(e, "Maligner", "fillScoreMatrix");
+ m->errorOut(e, "Maligner", "fillScoreMatrix");
exit(1);
}
}
+
//***************************************************************************************************************
-vector<score_struct> Maligner::extractHighestPath(vector<vector<score_struct> > m) {
+
+vector<trace_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
try {
+
//get matrix dimensions
int numCols = query->getAligned().length();
- int numRows = m.size();
+ int numRows = ms.size();
//find highest score scoring matrix
- score_struct highestStruct;
+ vector<score_struct> highestStruct;
int highestScore = 0;
for (int i = 0; i < numRows; i++) {
for (int j = 0; j < numCols; j++) {
- if (m[i][j].score > highestScore) {
- highestScore = m[i][j].score;
- highestStruct = m[i][j];
+ if (ms[i][j].score > highestScore) {
+ highestScore = ms[i][j].score;
+ highestStruct.resize(0);
+ highestStruct.push_back(ms[i][j]);
+ }
+ else if(ms[i][j].score == highestScore){
+ highestStruct.push_back(ms[i][j]);
}
}
}
-
- vector<score_struct> path;
+
+ //cout << endl << highestScore << '\t' << highestStruct.size() << '\t' << highestStruct[0].row << endl;
- int rowIndex = highestStruct.row;
- int pos = highestStruct.col;
- int score = highestStruct.score;
+ vector<trace_struct> maxTrace;
+ double maxPercentIdenticalQueryAntiChimera = 0;
- while (pos >= 0 && score > 0) {
- score_struct temp = m[rowIndex][pos];
- score = temp.score;
+ for(int i=0;i<highestStruct.size();i++){
- if (score > 0) { path.push_back(temp); }
+ vector<score_struct> path;
+
+ int rowIndex = highestStruct[i].row;
+ int pos = highestStruct[i].col;
+ int score = highestStruct[i].score;
+
+ while (pos >= 0 && score > 0) {
+ score_struct temp = ms[rowIndex][pos];
+ score = temp.score;
+
+ if (score > 0) { path.push_back(temp); }
+
+ rowIndex = temp.prev;
+ pos--;
+ }
+
+ reverse(path.begin(), path.end());
+
+ vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
+
+ //cout << "traces\n";
+ //for(int j=0;j<trace.size();j++){
+ // cout << trace[j].col << '\t' << trace[j].oldCol << '\t' << refSeqs[trace[j].row]->getName() << endl;
+ //}
+
+ int traceStart = path[0].col;
+ int traceEnd = path[path.size()-1].col;
+// cout << "traceStart/End\t" << traceStart << '\t' << traceEnd << endl;
- rowIndex = temp.prev;
- pos--;
+ string queryInRange = query->getAligned();
+ queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
+// cout << "here" << endl;
+ string chimeraSeq = constructChimericSeq(trace, refSeqs);
+ string antiChimeraSeq = constructAntiChimericSeq(trace, refSeqs);
+
+ percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
+ double percentIdenticalQueryAntiChimera = computePercentID(queryInRange, antiChimeraSeq);
+// cout << i << '\t' << percentIdenticalQueryChimera << '\t' << percentIdenticalQueryAntiChimera << endl;
+
+ if(percentIdenticalQueryAntiChimera > maxPercentIdenticalQueryAntiChimera){
+ maxPercentIdenticalQueryAntiChimera = percentIdenticalQueryAntiChimera;
+ maxTrace = trace;
+ }
}
-
- reverse(path.begin(), path.end());
+// cout << maxPercentIdenticalQueryAntiChimera << endl;
+ return maxTrace;
- return path;
}
catch(exception& e) {
- errorOut(e, "Maligner", "extractHighestPath");
+ m->errorOut(e, "Maligner", "extractHighestPath");
exit(1);
}
}
+
//***************************************************************************************************************
+
vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path, vector<Sequence*> seqs) {
try {
vector<trace_struct> trace;
temp.row = region_index;
trace.push_back(temp);
+// cout << endl;
+// cout << trace.size() << endl;
+// for(int i=0;i<trace.size();i++){
+// cout << seqs[trace[i].row]->getName() << endl;
+// }
+// cout << endl;
+
return trace;
}
catch(exception& e) {
- errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
+ m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
exit(1);
}
}
+
//***************************************************************************************************************
+
string Maligner::constructChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
try {
string chimera = "";
for (int i = 0; i < trace.size(); i++) {
+// cout << i << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
+
string seqAlign = seqs[trace[i].row]->getAligned();
seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
chimera += seqAlign;
return chimera;
}
catch(exception& e) {
- errorOut(e, "Maligner", "constructChimericSeq");
+ m->errorOut(e, "Maligner", "constructChimericSeq");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+string Maligner::constructAntiChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
+ try {
+ string antiChimera = "";
+
+ for (int i = 0; i < trace.size(); i++) {
+// cout << i << '\t' << (trace.size() - i - 1) << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl;
+
+ int oppositeIndex = trace.size() - i - 1;
+
+ string seqAlign = seqs[trace[oppositeIndex].row]->getAligned();
+ seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
+ antiChimera += seqAlign;
+ }
+
+ return antiChimera;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "constructChimericSeq");
exit(1);
}
}
+
//***************************************************************************************************************
float Maligner::computePercentID(string queryAlign, string chimera) {
try {
if (queryAlign.length() != chimera.length()) {
- mothurOut("Error, alignment strings are of different lengths: "); mothurOutEndLine();
- mothurOut(toString(queryAlign.length())); mothurOutEndLine(); mothurOutEndLine(); mothurOutEndLine(); mothurOutEndLine();
- mothurOut(toString(chimera.length())); mothurOutEndLine();
+ m->mothurOut("Error, alignment strings are of different lengths: "); m->mothurOutEndLine();
+ m->mothurOut(toString(queryAlign.length())); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOutEndLine();
+ m->mothurOut(toString(chimera.length())); m->mothurOutEndLine();
return -1.0;
}
-
- int numBases = 0;
int numIdentical = 0;
-
+ int countA = 0;
+ int countB = 0;
for (int i = 0; i < queryAlign.length(); i++) {
- if ((isalpha(queryAlign[i])) || (isalpha(chimera[i]))) {
- numBases++;
- if (queryAlign[i] == chimera[i]) {
- numIdentical++;
+ if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
+ ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
+ else {
+
+ bool charA = false; bool charB = false;
+ if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
+ if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
+
+ if (charA || charB) {
+
+ if (charA) { countA++; }
+ if (charB) { countB++; }
+
+ if (queryAlign[i] == chimera[i]) {
+ numIdentical++;
+ }
}
}
}
-
+
+ float numBases = (countA + countB) /(float) 2;
+
if (numBases == 0) { return 0; }
float percentIdentical = (numIdentical/(float)numBases) * 100;
}
catch(exception& e) {
- errorOut(e, "Maligner", "computePercentID");
+ m->errorOut(e, "Maligner", "computePercentID");
exit(1);
}
}
//***************************************************************************************************************
-
projects / mothur.git / blobdiff