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){
65 chimeraRefSeq = referenceSeqs[bestMatch];
70 chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
72 // minMismatchToTrimera = getTrimera(left, right, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight);
74 // if(minMismatchToChimera - minMismatchToTrimera <= 3){
76 // chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
80 // chimeraRefSeq = stitchTrimera(leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB);
84 double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
86 // double loonIndex = calcLoonIndex(querySeq, referenceSeqs[leftParentBi], referenceSeqs[rightParentBi], breakPointBi, binMatrix);
88 chimeraReportFile << queryName << '\t' << referenceNames[bestMatch] << '\t' << bestSequenceMismatch << '\t';
89 chimeraReportFile << referenceNames[leftParentBi] << ',' << referenceNames[rightParentBi] << '\t' << breakPointBi << '\t';
90 chimeraReportFile << minMismatchToChimera << '\t';
93 // chimeraReportFile << "NA" << '\t' << "NA" << '\t' << "NA";
96 // chimeraReportFile << referenceNames[leftParentTri] << ',' << referenceNames[middleParentTri] << ',' << referenceNames[rightParentTri] << '\t' << breakPointTriA << ',' << breakPointTriB << '\t' << minMismatchToTrimera;
99 chimeraReportFile << '\t' << distToChimera << '\t' << nMera << endl;
104 /**************************************************************************************************/
106 int RefChimeraTest::getMismatches(string& querySeq, vector<vector<int> >& left, vector<vector<int> >& right, int& bestRefSeq){
108 int bestSequenceMismatch = MAXINT;
110 for(int i=0;i<numRefSeqs;i++){
113 for(int l=0;l<alignLength;l++){
114 // if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
115 if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
123 for(int l=alignLength-1;l>=0;l--){
124 // if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
125 if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
128 right[i][index++] = rDiffs;
130 if(lDiffs < bestSequenceMismatch){
131 bestSequenceMismatch = lDiffs;
135 return bestSequenceMismatch;
138 /**************************************************************************************************/
140 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){
142 singleLeft.resize(alignLength, MAXINT);
143 bestLeft.resize(alignLength, -1);
145 for(int l=0;l<alignLength;l++){
146 for(int i=0;i<numRefSeqs;i++){
147 if(left[i][l] <= singleLeft[l]){
148 singleLeft[l] = left[i][l];
154 singleRight.resize(alignLength, MAXINT);
155 bestRight.resize(alignLength, -1);
157 for(int l=0;l<alignLength;l++){
158 for(int i=0;i<numRefSeqs;i++){
159 if(right[i][l] <= singleRight[l]){
160 singleRight[l] = right[i][l];
166 int bestChimeraMismatches = MAXINT;
171 for(int l=0;l<alignLength;l++){
172 int chimera = singleLeft[l] + singleRight[alignLength - l - 1];
173 if(chimera < bestChimeraMismatches){
174 bestChimeraMismatches = chimera;
176 leftParent = bestLeft[l];
177 rightParent = bestRight[alignLength - l - 1];
181 return bestChimeraMismatches;
184 /**************************************************************************************************/
186 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){
188 int bestTrimeraMismatches = MAXINT;
197 vector<vector<int> > minDelta(alignLength);
198 vector<vector<int> > minDeltaSeq(alignLength);
200 for(int i=0;i<alignLength;i++){
201 minDelta[i].assign(alignLength, MAXINT);
202 minDeltaSeq[i].assign(alignLength, -1);
205 for(int x=0;x<alignLength;x++){
206 for(int y=x;y<alignLength-1;y++){
208 for(int i=0;i<numRefSeqs;i++){
209 int delta = left[i][y] - left[i][x];
211 if(delta <= minDelta[x][y]){
212 minDelta[x][y] = delta;
213 minDeltaSeq[x][y] = i;
216 minDelta[x][y] += singleLeft[x] + singleRight[alignLength - y - 2];
218 if(minDelta[x][y] < bestTrimeraMismatches){
219 bestTrimeraMismatches = minDelta[x][y];
224 leftParent = bestLeft[x];
225 middleParent = minDeltaSeq[x][y];
226 rightParent = bestRight[alignLength - y - 2];
230 return bestTrimeraMismatches;
233 /**************************************************************************************************/
235 string RefChimeraTest::stitchBimera(int leftParent, int rightParent, int breakPoint){
237 string chimeraRefSeq = referenceSeqs[leftParent].substr(0, breakPoint) + referenceSeqs[rightParent].substr(breakPoint);
238 return chimeraRefSeq;
242 /**************************************************************************************************/
244 string RefChimeraTest::stitchTrimera(int leftParent, int middleParent, int rightParent, int breakPointA, int breakPointB){
246 string chimeraRefSeq = referenceSeqs[leftParent].substr(0, breakPointA) + referenceSeqs[middleParent].substr(breakPointA, breakPointB-breakPointA) + referenceSeqs[rightParent].substr(breakPointB);
248 return chimeraRefSeq;
251 /**************************************************************************************************/
253 double RefChimeraTest::calcDistToChimera(string& querySeq, string& chimeraRefSeq){
258 for(int i=0;i<alignLength;i++){
259 // if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
260 if(chimeraRefSeq[i] != '.'){
261 if(querySeq[i] == '-' && chimeraRefSeq[i] == '-'){ /* do nothing */ }
262 else if(querySeq[i] == chimeraRefSeq[i]){
271 return (double)mismatch / (double)(mismatch + match);
274 //***************************************************************************************************************
276 int RefChimeraTest::getClosestRefIndex(){
282 //***************************************************************************************************************