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++){
116 for(int l=0;l<alignLength;l++){
117 // if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
119 if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l] && referenceSeqs[i][l] != 'N'){
127 for(int l=alignLength-1;l>=0;l--){
128 // if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
129 if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l] && referenceSeqs[i][l] != 'N'){
132 right[i][index++] = rDiffs;
135 if(lDiffs < bestSequenceMismatch){
136 bestSequenceMismatch = lDiffs;
140 return bestSequenceMismatch;
143 /**************************************************************************************************/
145 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){
147 singleLeft.resize(alignLength, MAXINT);
148 bestLeft.resize(alignLength, -1);
150 for(int l=0;l<alignLength;l++){
151 for(int i=0;i<numRefSeqs;i++){
152 if(left[i][l] <= singleLeft[l]){
153 singleLeft[l] = left[i][l];
159 singleRight.resize(alignLength, MAXINT);
160 bestRight.resize(alignLength, -1);
162 for(int l=0;l<alignLength;l++){
163 for(int i=0;i<numRefSeqs;i++){
164 if(right[i][l] <= singleRight[l]){
165 singleRight[l] = right[i][l];
171 int bestChimeraMismatches = MAXINT;
176 for(int l=0;l<alignLength;l++){
177 int chimera = singleLeft[l] + singleRight[alignLength - l - 1];
178 if(chimera < bestChimeraMismatches){
179 bestChimeraMismatches = chimera;
181 leftParent = bestLeft[l];
182 rightParent = bestRight[alignLength - l - 1];
186 return bestChimeraMismatches;
189 /**************************************************************************************************/
191 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){
193 int bestTrimeraMismatches = MAXINT;
202 vector<vector<int> > minDelta(alignLength);
203 vector<vector<int> > minDeltaSeq(alignLength);
205 for(int i=0;i<alignLength;i++){
206 minDelta[i].assign(alignLength, MAXINT);
207 minDeltaSeq[i].assign(alignLength, -1);
210 for(int x=0;x<alignLength;x++){
211 for(int y=x;y<alignLength-1;y++){
213 for(int i=0;i<numRefSeqs;i++){
214 int delta = left[i][y] - left[i][x];
216 if(delta <= minDelta[x][y]){
217 minDelta[x][y] = delta;
218 minDeltaSeq[x][y] = i;
221 minDelta[x][y] += singleLeft[x] + singleRight[alignLength - y - 2];
223 if(minDelta[x][y] < bestTrimeraMismatches){
224 bestTrimeraMismatches = minDelta[x][y];
229 leftParent = bestLeft[x];
230 middleParent = minDeltaSeq[x][y];
231 rightParent = bestRight[alignLength - y - 2];
235 return bestTrimeraMismatches;
238 /**************************************************************************************************/
240 string RefChimeraTest::stitchBimera(int leftParent, int rightParent, int breakPoint){
242 string chimeraRefSeq = referenceSeqs[leftParent].substr(0, breakPoint) + referenceSeqs[rightParent].substr(breakPoint);
243 return chimeraRefSeq;
247 /**************************************************************************************************/
249 string RefChimeraTest::stitchTrimera(int leftParent, int middleParent, int rightParent, int breakPointA, int breakPointB){
251 string chimeraRefSeq = referenceSeqs[leftParent].substr(0, breakPointA) + referenceSeqs[middleParent].substr(breakPointA, breakPointB-breakPointA) + referenceSeqs[rightParent].substr(breakPointB);
253 return chimeraRefSeq;
256 /**************************************************************************************************/
258 double RefChimeraTest::calcDistToChimera(string& querySeq, string& chimeraRefSeq){
263 for(int i=0;i<alignLength;i++){
264 // if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
265 if(chimeraRefSeq[i] != '.' && querySeq[i] != '.'){
266 if(querySeq[i] == '-' && chimeraRefSeq[i] == '-' && chimeraRefSeq[i] != 'N'){ /* do nothing */ }
267 else if(querySeq[i] == chimeraRefSeq[i]){
276 return (double)mismatch / (double)(mismatch + match);
279 //***************************************************************************************************************
281 int RefChimeraTest::getClosestRefIndex(){
287 //***************************************************************************************************************