5 * Created by Pat Schloss on 1/31/11.
6 * Copyright 2011 Schloss Lab. All rights reserved.
10 #include "refchimeratest.h"
13 int MAXINT = numeric_limits<int>::max();
15 //***************************************************************************************************************
17 RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, string chimeraReportFileName){
19 m = MothurOut::getInstance();
21 m->openOutputFile(chimeraReportFileName, chimeraReportFile);
22 numRefSeqs = refs.size();
24 referenceSeqs.resize(numRefSeqs);
25 referenceNames.resize(numRefSeqs);
26 for(int i=0;i<numRefSeqs;i++){
27 referenceSeqs[i] = refs[i].getAligned();
28 referenceNames[i] = refs[i].getName();
31 alignLength = referenceSeqs[0].length();
33 chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents" << endl;
34 // chimeraReportFile << "leftParentTri,middleParentTri,rightParentTri\tbreakPointTriA,breakPointTriB\tminMismatchToTrimera\tdistToBestMera\tnMera" << endl;
38 //***************************************************************************************************************
40 int RefChimeraTest::analyzeQuery(string queryName, string querySeq){
42 vector<vector<int> > left(numRefSeqs);
43 vector<int> singleLeft, bestLeft;
44 vector<int> singleRight, bestRight;
46 vector<vector<int> > right(numRefSeqs);
47 for(int i=0;i<numRefSeqs;i++){
48 left[i].assign(alignLength, 0);
52 int bestSequenceMismatch = getMismatches(querySeq, left, right, bestMatch);
54 int leftParentBi, rightParentBi, breakPointBi;
55 int minMismatchToChimera = getChimera(left, right, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight);
57 // int minMismatchToTrimera = MAXINT;
58 // int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
61 string chimeraRefSeq = "";
63 if(bestSequenceMismatch - minMismatchToChimera > 3 || (minMismatchToChimera == 0 && bestSequenceMismatch != 0)){
66 chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
68 // minMismatchToTrimera = getTrimera(left, right, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight);
70 // if(minMismatchToChimera - minMismatchToTrimera <= 3){
72 // chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
76 // chimeraRefSeq = stitchTrimera(leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB);
82 chimeraRefSeq = referenceSeqs[bestMatch];
86 double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
88 // double loonIndex = calcLoonIndex(querySeq, referenceSeqs[leftParentBi], referenceSeqs[rightParentBi], breakPointBi, binMatrix);
90 chimeraReportFile << queryName << '\t' << referenceNames[bestMatch] << '\t' << bestSequenceMismatch << '\t';
91 chimeraReportFile << referenceNames[leftParentBi] << ',' << referenceNames[rightParentBi] << '\t' << breakPointBi << '\t';
92 chimeraReportFile << minMismatchToChimera << '\t';
95 // chimeraReportFile << "NA" << '\t' << "NA" << '\t' << "NA";
98 // chimeraReportFile << referenceNames[leftParentTri] << ',' << referenceNames[middleParentTri] << ',' << referenceNames[rightParentTri] << '\t' << breakPointTriA << ',' << breakPointTriB << '\t' << minMismatchToTrimera;
101 chimeraReportFile << '\t' << distToChimera << '\t' << nMera << endl;
106 /**************************************************************************************************/
108 int RefChimeraTest::getMismatches(string& querySeq, vector<vector<int> >& left, vector<vector<int> >& right, int& bestRefSeq){
110 int bestSequenceMismatch = MAXINT;
112 for(int i=0;i<numRefSeqs;i++){
115 for(int l=0;l<alignLength;l++){
116 // if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
117 if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
125 for(int l=alignLength-1;l>=0;l--){
126 // if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
127 if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
130 right[i][index++] = rDiffs;
132 if(lDiffs < bestSequenceMismatch){
133 bestSequenceMismatch = lDiffs;
137 return bestSequenceMismatch;
140 /**************************************************************************************************/
142 int RefChimeraTest::getChimera(vector<vector<int> >& left, vector<vector<int> >& right, int& leftParent, int& rightParent, int& breakPoint, vector<int>& singleLeft, vector<int>& bestLeft, vector<int>& singleRight, vector<int>& bestRight){
144 singleLeft.resize(alignLength, MAXINT);
145 bestLeft.resize(alignLength, -1);
147 for(int l=0;l<alignLength;l++){
148 for(int i=0;i<numRefSeqs;i++){
149 if(left[i][l] <= singleLeft[l]){
150 singleLeft[l] = left[i][l];
156 singleRight.resize(alignLength, MAXINT);
157 bestRight.resize(alignLength, -1);
159 for(int l=0;l<alignLength;l++){
160 for(int i=0;i<numRefSeqs;i++){
161 if(right[i][l] <= singleRight[l]){
162 singleRight[l] = right[i][l];
168 int bestChimeraMismatches = MAXINT;
173 for(int l=0;l<alignLength;l++){
174 int chimera = singleLeft[l] + singleRight[alignLength - l - 1];
175 if(chimera < bestChimeraMismatches){
176 bestChimeraMismatches = chimera;
178 leftParent = bestLeft[l];
179 rightParent = bestRight[alignLength - l - 1];
183 return bestChimeraMismatches;
186 /**************************************************************************************************/
188 int RefChimeraTest::getTrimera(vector<vector<int> >& left, vector<vector<int> >& right, int& leftParent, int& middleParent, int& rightParent, int& breakPointA, int& breakPointB, vector<int>& singleLeft, vector<int>& bestLeft, vector<int>& singleRight, vector<int>& bestRight){
190 int bestTrimeraMismatches = MAXINT;
199 vector<vector<int> > minDelta(alignLength);
200 vector<vector<int> > minDeltaSeq(alignLength);
202 for(int i=0;i<alignLength;i++){
203 minDelta[i].assign(alignLength, MAXINT);
204 minDeltaSeq[i].assign(alignLength, -1);
207 for(int x=0;x<alignLength;x++){
208 for(int y=x;y<alignLength-1;y++){
210 for(int i=0;i<numRefSeqs;i++){
211 int delta = left[i][y] - left[i][x];
213 if(delta <= minDelta[x][y]){
214 minDelta[x][y] = delta;
215 minDeltaSeq[x][y] = i;
218 minDelta[x][y] += singleLeft[x] + singleRight[alignLength - y - 2];
220 if(minDelta[x][y] < bestTrimeraMismatches){
221 bestTrimeraMismatches = minDelta[x][y];
226 leftParent = bestLeft[x];
227 middleParent = minDeltaSeq[x][y];
228 rightParent = bestRight[alignLength - y - 2];
232 return bestTrimeraMismatches;
235 /**************************************************************************************************/
237 string RefChimeraTest::stitchBimera(int leftParent, int rightParent, int breakPoint){
239 string chimeraRefSeq = referenceSeqs[leftParent].substr(0, breakPoint) + referenceSeqs[rightParent].substr(breakPoint);
240 return chimeraRefSeq;
244 /**************************************************************************************************/
246 string RefChimeraTest::stitchTrimera(int leftParent, int middleParent, int rightParent, int breakPointA, int breakPointB){
248 string chimeraRefSeq = referenceSeqs[leftParent].substr(0, breakPointA) + referenceSeqs[middleParent].substr(breakPointA, breakPointB-breakPointA) + referenceSeqs[rightParent].substr(breakPointB);
250 return chimeraRefSeq;
253 /**************************************************************************************************/
255 double RefChimeraTest::calcDistToChimera(string& querySeq, string& chimeraRefSeq){
260 for(int i=0;i<alignLength;i++){
261 // if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
262 if(chimeraRefSeq[i] != '.'){
263 if(querySeq[i] == '-' && chimeraRefSeq[i] == '-'){ /* do nothing */ }
264 else if(querySeq[i] == chimeraRefSeq[i]){
273 return (double)mismatch / (double)(mismatch + match);
276 //***************************************************************************************************************
278 int RefChimeraTest::getClosestRefIndex(){
284 //***************************************************************************************************************