5 * Created by Sarah Westcott on 7/9/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "bellerophon.h"
11 #include "eachgapdist.h"
12 #include "ignoregaps.h"
13 #include "onegapdist.h"
16 //***************************************************************************************************************
18 Bellerophon::Bellerophon(string name, string o) {
24 errorOut(e, "Bellerophon", "Bellerophon");
29 //***************************************************************************************************************
30 void Bellerophon::print(ostream& out) {
33 out << "Name\tScore\tLeft\tRight\t" << endl;
34 //output prefenence structure to .chimeras file
35 for (int i = 0; i < pref.size(); i++) {
36 out << pref[i].name << '\t' << setprecision(3) << pref[i].score[0] << '\t' << pref[i].leftParent[0] << '\t' << pref[i].rightParent[0] << endl;
38 //calc # of seqs with preference above 1.0
39 if (pref[i].score[0] > 1.0) {
41 mothurOut(pref[i].name + " is a suspected chimera at breakpoint " + toString(pref[i].midpoint)); mothurOutEndLine();
42 mothurOut("It's score is " + toString(pref[i].score[0]) + " with suspected left parent " + pref[i].leftParent[0] + " and right parent " + pref[i].rightParent[0]); mothurOutEndLine();
46 //output results to screen
48 mothurOut("Sequence with preference score above 1.0: " + toString(above1)); mothurOutEndLine();
51 mothurOut("Minimum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
52 spot = pref.size() * 0.975;
53 mothurOut("2.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
54 spot = pref.size() * 0.75;
55 mothurOut("25%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
56 spot = pref.size() * 0.50;
57 mothurOut("Median: \t" + toString(pref[spot].score[0])); mothurOutEndLine();
58 spot = pref.size() * 0.25;
59 mothurOut("75%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
60 spot = pref.size() * 0.025;
61 mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
63 mothurOut("Maximum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
67 errorOut(e, "Bellerophon", "print");
72 //********************************************************************************************************************
73 //sorts highest score to lowest
74 inline bool comparePref(Preference left, Preference right){
75 return (left.score[0] > right.score[0]);
78 //***************************************************************************************************************
79 int Bellerophon::getChimeras() {
84 string optionString = "fasta=" + fastafile + ", soft=50";
85 if (outputDir != "") { optionString += ", outputdir=" + outputDir; }
87 filterSeqs = new FilterSeqsCommand(optionString);
88 filterSeqs->execute();
91 //reset fastafile to filtered file
92 if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; }
93 else { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; }
97 distCalculator = new eachGapDist();
100 seqs = readSeqs(fastafile);
102 if (unaligned) { mothurOut("Your sequences need to be aligned when you use the bellerophon method."); mothurOutEndLine(); return 1; }
104 int numSeqs = seqs.size();
106 if (numSeqs == 0) { mothurOut("Error in reading you sequences."); mothurOutEndLine(); exit(1); }
108 //set default window to 25% of sequence length
109 string seq0 = seqs[0]->getAligned();
110 if (window == 0) { window = seq0.length() / 4; }
111 else if (window > (seq0.length() / 2)) {
112 mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); mothurOutEndLine();
113 window = (seq0.length() / 2);
116 if (increment > (seqs[0]->getAlignLength() - (2*window))) {
117 if (increment != 10) {
119 mothurOut("You have selected a increment that is too large. I will use the default."); mothurOutEndLine();
121 if (increment > (seqs[0]->getAlignLength() - (2*window))) { increment = 0; }
123 }else{ increment = 0; }
126 if (increment == 0) { iters = 1; }
127 else { iters = ((seqs[0]->getAlignLength() - (2*window)) / increment); }
130 pref.resize(numSeqs);
132 for (int i = 0; i < numSeqs; i++ ) {
133 pref[i].leftParent.resize(2); pref[i].rightParent.resize(2); pref[i].score.resize(2); pref[i].closestLeft.resize(2); pref[i].closestRight.resize(3);
134 pref[i].name = seqs[i]->getName();
135 pref[i].score[0] = 0.0; pref[i].score[1] = 0.0;
136 pref[i].closestLeft[0] = 100000.0; pref[i].closestLeft[1] = 100000.0;
137 pref[i].closestRight[0] = 100000.0; pref[i].closestRight[1] = 100000.0;
140 int midpoint = window;
142 while (count < iters) {
144 //create 2 vectors of sequences, 1 for left side and one for right side
145 vector<Sequence> left; vector<Sequence> right;
147 for (int i = 0; i < seqs.size(); i++) {
148 //cout << "midpoint = " << midpoint << "\twindow = " << window << endl;
149 //cout << "whole = " << seqs[i]->getAligned().length() << endl;
151 string seqLeft = seqs[i]->getAligned().substr(midpoint-window, window);
153 tempLeft.setName(seqs[i]->getName());
154 tempLeft.setAligned(seqLeft);
155 left.push_back(tempLeft);
156 //cout << "left = " << tempLeft.getAligned().length() << endl;
158 string seqRight = seqs[i]->getAligned().substr(midpoint, window);
160 tempRight.setName(seqs[i]->getName());
161 tempRight.setAligned(seqRight);
162 right.push_back(tempRight);
163 //cout << "right = " << seqRight.length() << endl;
166 //adjust midpoint by increment
167 midpoint += increment;
170 //this should be parallelized
171 //perference = sum of (| distance of my left to sequence j's left - distance of my right to sequence j's right | )
172 //create a matrix containing the distance from left to left and right to right
173 //calculate distances
174 SparseMatrix* SparseLeft = new SparseMatrix();
175 SparseMatrix* SparseRight = new SparseMatrix();
177 createSparseMatrix(0, left.size(), SparseLeft, left);
178 createSparseMatrix(0, right.size(), SparseRight, right);
180 vector<SeqMap> distMapRight;
181 vector<SeqMap> distMapLeft;
183 // Create a data structure to quickly access the distance information.
184 //this is from thallingers reimplementation on get.oturep
185 // It consists of a vector of distance maps, where each map contains
186 // all distances of a certain sequence. Vector and maps are accessed
187 // via the index of a sequence in the distance matrix
188 distMapRight = vector<SeqMap>(numSeqs);
189 distMapLeft = vector<SeqMap>(numSeqs);
190 //cout << "left" << endl << endl;
191 for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
192 distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
193 //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
195 //cout << "right" << endl << endl;
196 for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
197 distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
198 //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
204 //fill preference structure
205 generatePreferences(distMapLeft, distMapRight, midpoint);
211 delete distCalculator;
213 //rank preference score to eachother
215 float expectedPercent = 1 / (float) (pref.size());
217 for (int i = 0; i < pref.size(); i++) { dme += pref[i].score[0]; }
219 for (int i = 0; i < pref.size(); i++) {
221 //gives the actual percentage of the dme this seq adds
222 pref[i].score[0] = pref[i].score[0] / dme;
224 //how much higher or lower is this than expected
225 pref[i].score[0] = pref[i].score[0] / expectedPercent;
229 //sort Preferences highest to lowest
230 sort(pref.begin(), pref.end(), comparePref);
235 catch(exception& e) {
236 errorOut(e, "Bellerophon", "getChimeras");
241 /***************************************************************************************************************/
242 int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* sparse, vector<Sequence> s){
245 for(int i=startSeq; i<endSeq; i++){
247 for(int j=0;j<i;j++){
249 distCalculator->calcDist(s[i], s[j]);
250 float dist = distCalculator->getDist();
252 PCell temp(i, j, dist);
253 sparse->addCell(temp);
260 catch(exception& e) {
261 errorOut(e, "Bellerophon", "createSparseMatrix");
265 /***************************************************************************************************************/
266 void Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
270 SeqMap::iterator itR;
271 SeqMap::iterator itL;
274 for (int i = 0; i < pref.size(); i++) {
275 pref[i].score[1] = 0.0;
276 pref[i].closestLeft[1] = 100000.0;
277 pref[i].closestRight[1] = 100000.0;
278 pref[i].leftParent[1] = "";
279 pref[i].rightParent[1] = "";
282 for (int i = 0; i < left.size(); i++) {
284 SeqMap currentLeft = left[i]; //example i = 3; currentLeft is a map of 0 to the distance of sequence 3 to sequence 0,
285 // 1 to the distance of sequence 3 to sequence 1,
286 // 2 to the distance of sequence 3 to sequence 2.
287 SeqMap currentRight = right[i]; // same as left but with distances on the right side.
289 for (int j = 0; j < i; j++) {
291 itL = currentLeft.find(j);
292 itR = currentRight.find(j);
293 //cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
294 //cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
296 //if you can find this entry update the preferences
297 if ((itL != currentLeft.end()) && (itR != currentRight.end())) {
300 pref[i].score[1] += abs((itL->second - itR->second));
301 pref[j].score[1] += abs((itL->second - itR->second));
302 //cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
303 //cout << "abs = " << abs((itL->second - itR->second)) << endl;
304 //cout << i << " score = " << pref[i].score[1] << endl;
305 //cout << j << " score = " << pref[j].score[1] << endl;
307 pref[i].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
308 pref[j].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
309 //cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
310 //cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
311 //cout << i << " score = " << pref[i].score[1] << endl;
312 //cout << j << " score = " << pref[j].score[1] << endl;
314 //cout << "pref[" << i << "].closestLeft[1] = " << pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;
315 //are you the closest left sequence
316 if (itL->second < pref[i].closestLeft[1]) {
318 pref[i].closestLeft[1] = itL->second;
319 pref[i].leftParent[1] = seqs[j]->getName();
320 //cout << "updating closest left to " << pref[i].leftParent[1] << endl;
322 //cout << "pref[" << j << "].closestLeft[1] = " << pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;
323 if (itL->second < pref[j].closestLeft[1]) {
324 pref[j].closestLeft[1] = itL->second;
325 pref[j].leftParent[1] = seqs[i]->getName();
326 //cout << "updating closest left to " << pref[j].leftParent[1] << endl;
329 //are you the closest right sequence
330 if (itR->second < pref[i].closestRight[1]) {
331 pref[i].closestRight[1] = itR->second;
332 pref[i].rightParent[1] = seqs[j]->getName();
334 if (itR->second < pref[j].closestRight[1]) {
335 pref[j].closestRight[1] = itR->second;
336 pref[j].rightParent[1] = seqs[i]->getName();
348 for (int i = 0; i < pref.size(); i++) { dme += pref[i].score[1]; if (pref[i].score[1] == 0.0) { count0++; } }
350 float expectedPercent = 1 / (float) (pref.size() - count0);
351 //cout << endl << "dme = " << dme << endl;
352 //recalculate prefernences based on dme
353 for (int i = 0; i < pref.size(); i++) {
354 //cout << "unadjusted pref " << i << " = " << pref[i].score[1] << endl;
355 // gives the actual percentage of the dme this seq adds
356 pref[i].score[1] = pref[i].score[1] / dme;
358 //how much higher or lower is this than expected
359 pref[i].score[1] = pref[i].score[1] / expectedPercent;
361 //pref[i].score[1] = dme / (dme - 2 * pref[i].score[1]);
363 //so a non chimeric sequence would be around 1, and a chimeric would be signifigantly higher.
364 //cout << "adjusted pref " << i << " = " << pref[i].score[1] << endl;
367 //is this score bigger then the last score
368 for (int i = 0; i < pref.size(); i++) {
370 //update biggest score
371 if (pref[i].score[1] > pref[i].score[0]) {
372 pref[i].score[0] = pref[i].score[1];
373 pref[i].leftParent[0] = pref[i].leftParent[1];
374 pref[i].rightParent[0] = pref[i].rightParent[1];
375 pref[i].closestLeft[0] = pref[i].closestLeft[1];
376 pref[i].closestRight[0] = pref[i].closestRight[1];
377 pref[i].midpoint = mid;
383 catch(exception& e) {
384 errorOut(e, "Bellerophon", "generatePreferences");
388 /**************************************************************************************************/