X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=refchimeratest.cpp;fp=refchimeratest.cpp;h=2f397e8f71ec0b8a1d47338b1f12cfc552642ed2;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
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+/*
+ *  refchimeratest.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 1/31/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "refchimeratest.h"
+#include "mothur.h"
+
+int MAXINT = numeric_limits<int>::max();
+
+//***************************************************************************************************************
+
+RefChimeraTest::RefChimeraTest(vector<Sequence>& refs){
+
+	m = MothurOut::getInstance();
+
+	numRefSeqs = refs.size();
+
+	referenceSeqs.resize(numRefSeqs);
+	referenceNames.resize(numRefSeqs);
+	for(int i=0;i<numRefSeqs;i++){
+		referenceSeqs[i] = refs[i].getAligned();
+		referenceNames[i] = refs[i].getName();
+	}
+	
+	alignLength = referenceSeqs[0].length();
+
+
+}
+//***************************************************************************************************************
+
+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, ofstream& chimeraReportFile){
+	
+	vector<vector<int> > left(numRefSeqs);
+	vector<int> singleLeft, bestLeft;
+	vector<int> singleRight, bestRight;
+	
+	vector<vector<int> > right(numRefSeqs);
+	for(int i=0;i<numRefSeqs;i++){
+		left[i].assign(alignLength, 0);
+	}
+	right = left;
+	
+	int bestSequenceMismatch = getMismatches(querySeq, left, right, bestMatch);
+	
+	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 nMera = 0;
+	string chimeraRefSeq = "";
+	
+	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);
+//		}
+		
+	}
+	else{
+		nMera = 1;
+		chimeraRefSeq = referenceSeqs[bestMatch];
+	}
+	
+	
+	double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
+	
+//	double loonIndex = calcLoonIndex(querySeq, referenceSeqs[leftParentBi], referenceSeqs[rightParentBi], breakPointBi, binMatrix);		
+	
+	chimeraReportFile << queryName << '\t' << referenceNames[bestMatch] << '\t' << bestSequenceMismatch << '\t';
+	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;	
+//	}
+	
+	chimeraReportFile << '\t' << distToChimera << '\t' << nMera << endl;
+		
+	return nMera;
+}
+
+/**************************************************************************************************/
+
+int RefChimeraTest::getMismatches(string& querySeq, vector<vector<int> >& left, vector<vector<int> >& right, int& bestRefSeq){
+	
+	int bestSequenceMismatch = MAXINT;
+	
+	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] != '.' && 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] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l] && referenceSeqs[i][l] != 'N'){
+				rDiffs++;
+			}			
+			right[i][index++] = rDiffs;
+		}
+		
+		if(lDiffs < bestSequenceMismatch){
+			bestSequenceMismatch = lDiffs;
+			bestRefSeq = i;
+		}
+	}
+	return bestSequenceMismatch;
+}
+
+/**************************************************************************************************/
+
+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){
+	
+	singleLeft.resize(alignLength, MAXINT);
+	bestLeft.resize(alignLength, -1);
+	
+	for(int l=0;l<alignLength;l++){
+		for(int i=0;i<numRefSeqs;i++){
+			if(left[i][l] <= singleLeft[l]){
+				singleLeft[l] = left[i][l];
+				bestLeft[l] = i;
+			}
+		}
+	}
+	
+	singleRight.resize(alignLength, MAXINT);
+	bestRight.resize(alignLength, -1);
+	
+	for(int l=0;l<alignLength;l++){
+		for(int i=0;i<numRefSeqs;i++){
+			if(right[i][l] <= singleRight[l]){
+				singleRight[l] = right[i][l];
+				bestRight[l] = i;
+			}
+		}
+	}
+	
+	int bestChimeraMismatches = MAXINT;
+	leftParent = -1;
+	rightParent = -1;
+	breakPoint = -1;
+	
+	for(int l=0;l<alignLength;l++){
+		int chimera = singleLeft[l] + singleRight[alignLength - l - 1];
+		if(chimera < bestChimeraMismatches){
+			bestChimeraMismatches = chimera;
+			breakPoint = l;
+			leftParent = bestLeft[l];
+			rightParent = bestRight[alignLength - l - 1];
+		}
+	}
+	
+	return bestChimeraMismatches;
+}
+
+/**************************************************************************************************/
+
+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){
+	
+	int bestTrimeraMismatches = MAXINT;
+	
+	leftParent = -1;
+	middleParent = -1;
+	rightParent = -1;
+	
+	breakPointA = -1;
+	breakPointB = -1;
+	
+	vector<vector<int> > minDelta(alignLength);
+	vector<vector<int> > minDeltaSeq(alignLength);
+	
+	for(int i=0;i<alignLength;i++){
+		minDelta[i].assign(alignLength, MAXINT);
+		minDeltaSeq[i].assign(alignLength, -1);
+	}
+	
+	for(int x=0;x<alignLength;x++){
+		for(int y=x;y<alignLength-1;y++){
+			
+			for(int i=0;i<numRefSeqs;i++){
+				int delta = left[i][y] - left[i][x];
+				
+				if(delta <= minDelta[x][y]){
+					minDelta[x][y] = delta;
+					minDeltaSeq[x][y] = i;					
+				}				
+			}
+			minDelta[x][y] += singleLeft[x] + singleRight[alignLength - y - 2];
+			
+			if(minDelta[x][y] < bestTrimeraMismatches){
+				bestTrimeraMismatches = minDelta[x][y];
+				
+				breakPointA = x;
+				breakPointB = y;
+				
+				leftParent = bestLeft[x];
+				middleParent = minDeltaSeq[x][y];
+				rightParent = bestRight[alignLength - y - 2];				
+			}
+		}		
+	}
+	return bestTrimeraMismatches;
+}
+
+/**************************************************************************************************/
+
+string RefChimeraTest::stitchBimera(int leftParent, int rightParent, int breakPoint){
+	
+	string chimeraRefSeq = referenceSeqs[leftParent].substr(0, breakPoint) + referenceSeqs[rightParent].substr(breakPoint);
+	return chimeraRefSeq;
+	
+}
+
+/**************************************************************************************************/
+
+string RefChimeraTest::stitchTrimera(int leftParent, int middleParent, int rightParent, int breakPointA, int breakPointB){
+	
+	string chimeraRefSeq = referenceSeqs[leftParent].substr(0, breakPointA) + referenceSeqs[middleParent].substr(breakPointA, breakPointB-breakPointA) + referenceSeqs[rightParent].substr(breakPointB);
+	
+	return chimeraRefSeq;
+}
+
+/**************************************************************************************************/
+
+double RefChimeraTest::calcDistToChimera(string& querySeq, string& chimeraRefSeq){
+	
+	int match = 0;
+	int mismatch = 0;
+	
+	for(int i=0;i<alignLength;i++){
+//		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++;
+			}
+			else{
+				mismatch++;
+			}			
+		}
+	}
+	
+	return (double)mismatch / (double)(mismatch + match);	
+}
+
+//***************************************************************************************************************
+
+int RefChimeraTest::getClosestRefIndex(){
+
+	return bestMatch;
+	
+}
+
+//***************************************************************************************************************