//***************************************************************************************************************
-RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, string chimeraReportFileName){
+RefChimeraTest::RefChimeraTest(vector<Sequence>& refs){
m = MothurOut::getInstance();
- m->openOutputFile(chimeraReportFileName, chimeraReportFile);
numRefSeqs = refs.size();
referenceSeqs.resize(numRefSeqs);
alignLength = referenceSeqs[0].length();
- chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\t";
- chimeraReportFile << "leftParentChi,middleParentTri,rightParentChi\tbreakPointTriA,breakPointTriB\tminMismatchToTrimera\tdistToBestMera\tnMera" << endl;
}
+//***************************************************************************************************************
+int RefChimeraTest::printHeader(ofstream& chimeraReportFile){
+ try {
+ chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents" << endl;
+ return 0;
+ }catch(exception& e) {
+ m->errorOut(e, "RefChimeraTest", "execute");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-int RefChimeraTest::analyzeQuery(string queryName, string querySeq){
+int RefChimeraTest::analyzeQuery(string queryName, string querySeq, ofstream& chimeraReportFile){
vector<vector<int> > left(numRefSeqs);
vector<int> singleLeft, bestLeft;
int leftParentBi, rightParentBi, breakPointBi;
int minMismatchToChimera = getChimera(left, right, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight);
- int minMismatchToTrimera = MAXINT;
- int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
+// int minMismatchToTrimera = MAXINT;
+// int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
int nMera = 0;
string chimeraRefSeq = "";
- if(bestSequenceMismatch - minMismatchToChimera <= 3){
- nMera = 1;
- chimeraRefSeq = referenceSeqs[bestMatch];
- }
- else {
+ if(bestSequenceMismatch - minMismatchToChimera >= 3){// || (minMismatchToChimera == 0 && bestSequenceMismatch != 0)){
+
+ nMera = 2;
+ chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
- minMismatchToTrimera = getTrimera(left, right, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight);
-
- if(minMismatchToChimera - minMismatchToTrimera <= 3){
- nMera = 2;
- chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
- }
- else{
- nMera = 3;
- chimeraRefSeq = stitchTrimera(leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB);
- }
+// minMismatchToTrimera = getTrimera(left, right, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight);
+//
+// if(minMismatchToChimera - minMismatchToTrimera <= 3){
+// nMera = 2;
+// chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
+// }
+// else{
+// nMera = 3;
+// chimeraRefSeq = stitchTrimera(leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB);
+// }
}
+ else{
+ nMera = 1;
+ chimeraRefSeq = referenceSeqs[bestMatch];
+ }
+
+
double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
// double loonIndex = calcLoonIndex(querySeq, referenceSeqs[leftParentBi], referenceSeqs[rightParentBi], breakPointBi, binMatrix);
chimeraReportFile << referenceNames[leftParentBi] << ',' << referenceNames[rightParentBi] << '\t' << breakPointBi << '\t';
chimeraReportFile << minMismatchToChimera << '\t';
- if(nMera == 1){
- chimeraReportFile << "NA" << '\t' << "NA" << '\t' << "NA";
- }
- else{
- chimeraReportFile << referenceNames[leftParentTri] << ',' << referenceNames[middleParentTri] << ',' << referenceNames[rightParentTri] << '\t' << breakPointTriA << ',' << breakPointTriB << '\t' << minMismatchToTrimera;
- }
+// if(nMera == 1){
+// chimeraReportFile << "NA" << '\t' << "NA" << '\t' << "NA";
+// }
+// else{
+// chimeraReportFile << referenceNames[leftParentTri] << ',' << referenceNames[middleParentTri] << ',' << referenceNames[rightParentTri] << '\t' << breakPointTriA << ',' << breakPointTriB << '\t' << minMismatchToTrimera;
+// }
chimeraReportFile << '\t' << distToChimera << '\t' << nMera << endl;
for(int i=0;i<numRefSeqs;i++){
int lDiffs = 0;
+
for(int l=0;l<alignLength;l++){
- if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+// if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+
+ if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l] && referenceSeqs[i][l] != 'N'){
lDiffs++;
}
left[i][l] = lDiffs;
int rDiffs = 0;
int index = 0;
for(int l=alignLength-1;l>=0;l--){
- if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+// if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+ if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l] && referenceSeqs[i][l] != 'N'){
rDiffs++;
}
right[i][index++] = rDiffs;
}
+
if(lDiffs < bestSequenceMismatch){
bestSequenceMismatch = lDiffs;
bestRefSeq = i;
int mismatch = 0;
for(int i=0;i<alignLength;i++){
- if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
- if(querySeq[i] == '-' && chimeraRefSeq[i] == '-'){ /* do nothing */ }
+// if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
+ if(chimeraRefSeq[i] != '.' && querySeq[i] != '.'){
+ if(querySeq[i] == '-' && chimeraRefSeq[i] == '-' && chimeraRefSeq[i] != 'N'){ /* do nothing */ }
else if(querySeq[i] == chimeraRefSeq[i]){
match++;
}