*/
#include "chimeraseqscommand.h"
+#include "eachgapdist.h"
//***************************************************************************************************************
else {
//valid paramters for this command
- string Array[] = {"fasta", "filter", "correction", "processors", "method" };
+ string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment" };
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); mothurOutEndLine(); abort = true; }
string temp;
- temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
+ temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "T"; }
filter = isTrue(temp);
temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; }
correction = isTrue(temp);
- temp = validParameter.validFile(parameters, "processors", true); if (temp == "not found") { temp = "1"; }
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
convert(temp, processors);
+ temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, window);
+
+ temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, increment);
+
method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "bellerophon"; }
+
+ if (method != "bellerophon") { mothurOut(method + " is not a valid method."); mothurOutEndLine(); abort = true; }
}
}
exit(1);
}
}
+//********************************************************************************************************************
+//sorts highest score to lowest
+inline bool comparePref(Preference left, Preference right){
+ return (left.score[0] > right.score[0]);
+}
//***************************************************************************************************************
if (abort == true) { return 0; }
+
//do soft filter
if (filter) {
- string optionString = "fasta=" + fastafile + ", soft=50.0, vertical=F";
+ string optionString = "fasta=" + fastafile + ", soft=50, vertical=F";
filterSeqs = new FilterSeqsCommand(optionString);
filterSeqs->execute();
delete filterSeqs;
fastafile = getRootName(fastafile) + "filter.fasta";
}
+ distCalculator = new eachGapDist();
+
//read in sequences
readSeqs();
- //int numSeqs = seqs.size();
+ int numSeqs = seqs.size();
- //find average midpoint of seqs
- midpoint = findAverageMidPoint();
+ if (numSeqs == 0) { mothurOut("Error in reading you sequences."); mothurOutEndLine(); return 0; }
- //create 2 vectors of sequences, 1 for left side and one for right side
- vector<Sequence> left; vector<Sequence> right;
+ //set default window to 25% of sequence length
+ string seq0 = seqs[0].getAligned();
+ if (window == 0) { window = seq0.length() / 4; }
+ else if (window > (seq0.length() / 2)) {
+ 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();
+ window = (seq0.length() / 2);
+ }
- for (int i = 0; i < seqs.size(); i++) {
- //save left side
- string seqLeft = seqs[i].getAligned();
- seqLeft = seqLeft.substr(0, midpoint);
- Sequence tempLeft(seqs[i].getName(), seqLeft);
- left.push_back(tempLeft);
+ if (increment > (seqs[0].getAlignLength() - (2*window))) {
+ if (increment != 10) {
- //save right side
- string seqRight = seqs[i].getAligned();
- seqRight = seqRight.substr(midpoint+1, (seqRight.length()-midpoint-1));
- Sequence tempRight(seqs[i].getName(), seqRight);
- right.push_back(tempRight);
+ mothurOut("You have selected a increment that is too large. I will use the default."); mothurOutEndLine();
+ increment = 10;
+ if (increment > (seqs[0].getAlignLength() - (2*window))) { increment = 0; }
+
+ }else{ increment = 0; }
+ }
+cout << "increment = " << increment << endl;
+ if (increment == 0) { iters = 1; }
+ else { iters = ((seqs[0].getAlignLength() - (2*window)) / increment); }
+
+ //initialize pref
+ pref.resize(numSeqs);
+
+ for (int i = 0; i < numSeqs; i++ ) {
+ 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);
+ pref[i].name = seqs[i].getName();
+ pref[i].score[0] = 0.0; pref[i].score[1] = 0.0;
+ pref[i].closestLeft[0] = 100000.0; pref[i].closestLeft[1] = 100000.0;
+ pref[i].closestRight[0] = 100000.0; pref[i].closestRight[1] = 100000.0;
}
+
+ int midpoint = window;
+ int count = 0;
+ while (count < iters) {
+
+ //create 2 vectors of sequences, 1 for left side and one for right side
+ vector<Sequence> left; vector<Sequence> right;
+
+ for (int i = 0; i < seqs.size(); i++) {
+//cout << "whole = " << seqs[i].getAligned() << endl;
+ //save left side
+ string seqLeft = seqs[i].getAligned().substr(midpoint-window, window);
+ Sequence tempLeft;
+ tempLeft.setName(seqs[i].getName());
+ tempLeft.setAligned(seqLeft);
+ left.push_back(tempLeft);
+//cout << "left = " << tempLeft.getAligned() << endl;
+ //save right side
+ string seqRight = seqs[i].getAligned().substr(midpoint, window);
+ Sequence tempRight;
+ tempRight.setName(seqs[i].getName());
+ tempRight.setAligned(seqRight);
+ right.push_back(tempRight);
+//cout << "right = " << seqRight << endl;
+ }
+
+ //adjust midpoint by increment
+ midpoint += increment;
+
+
+ //this should be parallelized
+ //perference = sum of (| distance of my left to sequence j's left - distance of my right to sequence j's right | )
+ //create a matrix containing the distance from left to left and right to right
+ //calculate distances
+ SparseMatrix* SparseLeft = new SparseMatrix();
+ SparseMatrix* SparseRight = new SparseMatrix();
+
+ createSparseMatrix(0, left.size(), SparseLeft, left);
+ createSparseMatrix(0, right.size(), SparseRight, right);
+
+ vector<SeqMap> distMapRight;
+ vector<SeqMap> distMapLeft;
+
+ // Create a data structure to quickly access the distance information.
+ // It consists of a vector of distance maps, where each map contains
+ // all distances of a certain sequence. Vector and maps are accessed
+ // via the index of a sequence in the distance matrix
+ distMapRight = vector<SeqMap>(numSeqs);
+ distMapLeft = vector<SeqMap>(numSeqs);
+ //cout << "left" << endl << endl;
+ for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
+ distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
+ //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
+ }
+ //cout << "right" << endl << endl;
+ for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
+ distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
+ //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
+ }
+
+ delete SparseLeft;
+ delete SparseRight;
- //this should be parallelized
- //perference = sum of (| distance of my left to sequence j's left - distance of my right to sequence j's right | )
- //create a matrix containing the distance from left to left and right to right
- //calculate distances
- SparseMatrix* SparseLeft = new SparseMatrix();
- SparseMatrix* SparseRight = new SparseMatrix();
+
+ //fill preference structure
+ generatePreferences(distMapLeft, distMapRight, midpoint);
+
+ count++;
+
+ }
- createSparseMatrix(0, left.size(), SparseLeft, left);
- createSparseMatrix(0, right.size(), SparseRight, right);
+ delete distCalculator;
+ //find average pref score across windows
+ //if (increment != 0) {
+
+ //for (int i = 0; i < pref.size(); i++) {
+ //pref[i].score[0] = pref[i].score[0] / iters;
+ //}
+ //}
- //vector<SeqMap> distMapRight;
- //vector<SeqMap> distMapLeft;
+ //sort Preferences highest to lowest
+ sort(pref.begin(), pref.end(), comparePref);
- // Create a data structure to quickly access the distance information.
- // It consists of a vector of distance maps, where each map contains
- // all distances of a certain sequence. Vector and maps are accessed
- // via the index of a sequence in the distance matrix
- //distMapRight = vector<SeqMap>(globaldata->gListVector->size());
- //distMapLeft = vector<SeqMap>(globaldata->gListVector->size());
- for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
- //distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
- }
- for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
- //distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
- }
-
+ string outputFileName = getRootName(fastafile) + "chimeras";
+ ofstream out;
+ openOutputFile(outputFileName, out);
- //fill preference structure
- //generatePreferences(distMapLeft, distMapRight);
+ int above1 = 0;
+ out << "Name\tScore\tLeft\tRight\t" << endl;
+ //output prefenence structure to .chimeras file
+ for (int i = 0; i < pref.size(); i++) {
+ out << pref[i].name << '\t' << pref[i].score[0] << '\t' << pref[i].leftParent[0] << '\t' << pref[i].rightParent[0] << endl;
+
+ //calc # of seqs with preference above 1.0
+ if (pref[i].score[0] > 1.0) {
+ above1++;
+ mothurOut(pref[i].name + " is a suspected chimera at breakpoint " + toString(pref[i].midpoint)); mothurOutEndLine();
+ 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();
+ }
+
+
+ }
-
- //output results to screen
+ //output results to screen
mothurOutEndLine();
- mothurOut("\t\t"); mothurOutEndLine();
- //mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); mothurOutEndLine();
- //mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25])); mothurOutEndLine();
- //mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25])); mothurOutEndLine();
- //mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50])); mothurOutEndLine();
- //mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); mothurOutEndLine();
- //mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5])); mothurOutEndLine();
- //mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100])); mothurOutEndLine();
- //mothurOut("# of Seqs:\t" + toString(numSeqs)); mothurOutEndLine();
+ mothurOut("Sequence with preference score above 1.0: " + toString(above1)); mothurOutEndLine();
+ int spot;
+ spot = pref.size()-1;
+ mothurOut("Minimum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+ spot = pref.size() * 0.975;
+ mothurOut("2.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+ spot = pref.size() * 0.75;
+ mothurOut("25%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+ spot = pref.size() * 0.50;
+ mothurOut("Median: \t" + toString(pref[spot].score[0])); mothurOutEndLine();
+ spot = pref.size() * 0.25;
+ mothurOut("75%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+ spot = pref.size() * 0.025;
+ mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+ spot = 0;
+ mothurOut("Maximum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
- //outSummary.close();
return 0;
}
catch(exception& e) {
while(!inFASTA.eof()){
Sequence current(inFASTA);
+ if (current.getAligned() == "") { current.setAligned(current.getUnaligned()); }
+
seqs.push_back(current);
gobble(inFASTA);
}
}
-
-//***************************************************************************************************************
-int ChimeraSeqsCommand::findAverageMidPoint(){
- try {
- int totalMids = 0;
- int averageMid = 0;
-
- //loop through the seqs and find midpoint
- for (int i = 0; i < seqs.size(); i++) {
-
- //get unaligned sequence
- seqs[i].setUnaligned(seqs[i].getUnaligned()); //if you read an aligned file the unaligned is really aligned, so we need to make sure its unaligned
-
- string unaligned = seqs[i].getUnaligned();
- string aligned = seqs[i].getAligned();
-
- //find midpoint of this seq
- int count = 0;
- int thismid = 0;
- for (int j = 0; j < aligned.length(); j++) {
-
- thismid++;
-
- //if you are part of the unaligned sequence increment
- if (isalpha(aligned[j])) { count++; }
-
- //if you have reached the halfway point stop
- if (count >= (unaligned.length() / 2)) { break; }
- }
-
- //add this mid to total
- totalMids += thismid;
-
- }
-
- averageMid = (totalMids / seqs.size());
-
- return averageMid;
-
-
- }
- catch(exception& e) {
- errorOut(e, "ChimeraSeqsCommand", "findAverageMidPoint");
- exit(1);
- }
-}
-
/***************************************************************************************************************/
int ChimeraSeqsCommand::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* sparse, vector<Sequence> s){
try {
for(int j=0;j<i;j++){
- //distCalculator->calcDist(s.get(i), s.get(j));
+ distCalculator->calcDist(s[i], s[j]);
float dist = distCalculator->getDist();
-
+
PCell temp(i, j, dist);
sparse->addCell(temp);
exit(1);
}
}
-/***************************************************************************************************************
-void ChimeraSeqsCommand::generatePreferences(vector<SeqMap> left, vector<SeqMap> right){
+/***************************************************************************************************************/
+void ChimeraSeqsCommand::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
try {
+
+ float dme = 0.0;
+ SeqMap::iterator itR;
+ SeqMap::iterator itL;
+
+ //initialize pref[i]
+ for (int i = 0; i < pref.size(); i++) {
+ pref[i].score[1] = 0.0;
+ pref[i].closestLeft[1] = 100000.0;
+ pref[i].closestRight[1] = 100000.0;
+ pref[i].leftParent[1] = "";
+ pref[i].rightParent[1] = "";
+ }
+//cout << "in generate left.size() = " << left.size() << endl;
for (int i = 0; i < left.size(); i++) {
- int iscore = 0;
- float closestLeft = 100000.0;
- float closestRight = 100000.0;
+ SeqMap currentLeft = left[i]; //example i = 3; currentLeft is a map of 0 to the distance of sequence 3 to sequence 0,
+ // 1 to the distance of sequence 3 to sequence 1,
+ // 2 to the distance of sequence 3 to sequence 2.
+ SeqMap currentRight = right[i]; // same as left but with distances on the right side.
- for (int j = 0; j < left.size(); j++) {
+ for (int j = 0; j < i; j++) {
- //iscore += abs(left
-
+ itL = currentLeft.find(j);
+ itR = currentRight.find(j);
+cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
+cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
+
+ //if you can find this entry update the preferences
+ if ((itL != currentLeft.end()) && (itR != currentRight.end())) {
+
+ if (!correction) {
+ pref[i].score[1] += abs((itL->second - itR->second));
+ pref[j].score[1] += abs((itL->second - itR->second));
+cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
+cout << "abs = " << abs((itL->second - itR->second)) << endl;
+cout << i << " score = " << pref[i].score[1] << endl;
+cout << j << " score = " << pref[j].score[1] << endl;
+ }else {
+ pref[i].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
+ pref[j].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
+cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
+cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
+cout << i << " score = " << pref[i].score[1] << endl;
+cout << j << " score = " << pref[j].score[1] << endl;
+ }
+cout << "pref[" << i << "].closestLeft[1] = " << pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;
+ //are you the closest left sequence
+ if (itL->second < pref[i].closestLeft[1]) {
+
+ pref[i].closestLeft[1] = itL->second;
+ pref[i].leftParent[1] = seqs[j].getName();
+cout << "updating closest left to " << pref[i].leftParent[1] << endl;
+ }
+cout << "pref[" << j << "].closestLeft[1] = " << pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;
+ if (itL->second < pref[j].closestLeft[1]) {
+ pref[j].closestLeft[1] = itL->second;
+ pref[j].leftParent[1] = seqs[i].getName();
+cout << "updating closest left to " << pref[j].leftParent[1] << endl;
+ }
+
+ //are you the closest right sequence
+ if (itR->second < pref[i].closestRight[1]) {
+ pref[i].closestRight[1] = itR->second;
+ pref[i].rightParent[1] = seqs[j].getName();
+ }
+ if (itR->second < pref[j].closestRight[1]) {
+ pref[j].closestRight[1] = itR->second;
+ pref[j].rightParent[1] = seqs[i].getName();
+ }
+
+ }
}
}
+
+
+
+ //calculate the dme
+ int count0 = 0;
+ for (int i = 0; i < pref.size(); i++) { dme += pref[i].score[1]; if (pref[i].score[1] == 0.0) { count0++; } }
+
+ float expectedPercent = 1 / (float) (pref.size() - count0);
+cout << endl << "dme = " << dme << endl;
+ //recalculate prefernences based on dme
+ for (int i = 0; i < pref.size(); i++) {
+cout << "unadjusted pref " << i << " = " << pref[i].score[1] << endl;
+ // gives the actual percentage of the dme this seq adds
+ pref[i].score[1] = pref[i].score[1] / dme;
+
+ //how much higher or lower is this than expected
+ pref[i].score[1] = pref[i].score[1] / expectedPercent;
+
+ //so a non chimeric sequence would be around 1, and a chimeric would be signifigantly higher.
+cout << "adjusted pref " << i << " = " << pref[i].score[1] << endl;
+ }
+
+ //is this score bigger then the last score
+ for (int i = 0; i < pref.size(); i++) {
+
+ //update biggest score
+ if (pref[i].score[1] > pref[i].score[0]) {
+ pref[i].score[0] = pref[i].score[1];
+ pref[i].leftParent[0] = pref[i].leftParent[1];
+ pref[i].rightParent[0] = pref[i].rightParent[1];
+ pref[i].closestLeft[0] = pref[i].closestLeft[1];
+ pref[i].closestRight[0] = pref[i].closestRight[1];
+ pref[i].midpoint = mid;
+ }
+
+ //total of preference scores across windows
+ //pref[i].score[0] += pref[i].score[1];
+ }
}
catch(exception& e) {
projects / mothur.git / blobdiff