mothurOutEndLine();
+ string mapInfo = getRootName(fastafile) + "mapinfo";
+ ofstream out2;
+ openOutputFile(mapInfo, out2);
+
+ out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
+
+ for (int j = 0; j < querySeqs.size(); j++) {
+ out2 << querySeqs[j]->getName() << endl;
+ for (it = spotMap[j].begin(); it!= spotMap[j].end(); it++) {
+ out2 << it->first << '\t' << it->second << endl;
+ }
+ }
+ out2.close();
+
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ out << "For full window mapping info refer to " << mapInfo << endl << endl;
+
for (int i = 0; i < querySeqs.size(); i++) {
+
+ out << querySeqs[i]->getName() << endl << endl << "Reference sequences used and distance to query:" << endl;
+
+ for (int j = 0; j < closest[i].size(); j++) {
+ out << setprecision(3) << closest[i][j].seq->getName() << '\t' << closest[i][j].dist << endl;
+ }
+ out << endl << endl;
+
+ //for each window
+ //window mapping info.
+ out << "Mapping information: " << endl;
+ //you mask and did not filter
+ if ((seqMask != "") && (!filter)) { out << "mask and trim."; }
+
+ //you filtered and did not mask
+ if ((seqMask == "") && (filter)) { out << "filter and trim."; }
+
+ //you masked and filtered
+ if ((seqMask != "") && (filter)) { out << "mask, filter and trim."; }
+
+ out << "Window\tStartPos\tEndPos" << endl;
+ it = trim[i].begin();
+
+ for (int k = 0; k < windows[i].size()-1; k++) {
+ out << k+1 << '\t' << spotMap[i][windows[i][k]-it->first] << '\t' << spotMap[i][windows[i][k]-it->first+windowSizes[i]] << endl;
+ }
+
+ out << windows[i].size() << '\t' << spotMap[i][windows[i][windows[i].size()-1]-it->first] << '\t' << spotMap[i][it->second-it->first-1] << endl;
+ out << endl;
+
+ out << "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova" << endl;
+ for (int k = 0; k < windows[i].size(); k++) {
+ float ds = averageQuery[i][k] / averageRef[i][k];
+ out << k+1 << '\t' << averageQuery[i][k] << '\t' << sdQuery[i][k] << '\t' << averageRef[i][k] << '\t'<< sdRef[i][k] << '\t' << ds << '\t' << anova[i][k] << endl;
+ }
+ out << endl;
+ //varRef
+ //varQuery
+ /* F test for differences among variances.
+ * varQuery is expected to be higher or similar than varRef */
+ //float fs = varQuery[query][i] / varRef[query][i]; /* F-Snedecor, test for differences of variances */
+
+ bool results = false;
+
+ //confidence limit, t - Student, anova
+ out << "Window\tConfidenceLimit\tt-Student\tAnova" << endl;
+
+ for (int k = 0; k < windows[i].size(); k++) {
+ string temp = "";
+ if (isChimericConfidence[i][k]) { temp += "*\t"; }
+ else { temp += "\t"; }
+
+ if (isChimericTStudent[i][k]) { temp += "*\t"; }
+ else { temp += "\t"; }
+
+ if (isChimericANOVA[i][k]) { temp += "*\t"; }
+ else { temp += "\t"; }
+
+ out << k+1 << '\t' << temp << endl;
+
+ if (temp != "\t\t\t") { results = true; }
+ }
+ out << endl;
+
+ if (results) {
+ mothurOut(querySeqs[i]->getName() + " was found have at least one chimeric window."); mothurOutEndLine();
+ }
}
}
catch(exception& e) {
closest.resize(numSeqs);
+ refCombo.resize(numSeqs, 0);
+ sumRef.resize(numSeqs);
+ varRef.resize(numSeqs);
+ varQuery.resize(numSeqs);
+ sdRef.resize(numSeqs);
+ sdQuery.resize(numSeqs);
+ sumQuery.resize(numSeqs);
+ sumSquaredRef.resize(numSeqs);
+ sumSquaredQuery.resize(numSeqs);
+ averageRef.resize(numSeqs);
+ averageQuery.resize(numSeqs);
+ anova.resize(numSeqs);
+ isChimericConfidence.resize(numSeqs);
+ isChimericTStudent.resize(numSeqs);
+ isChimericANOVA.resize(numSeqs);
+ trim.resize(numSeqs);
+ spotMap.resize(numSeqs);
+ windowSizes.resize(numSeqs, window);
+ windows.resize(numSeqs);
+
//break up file if needed
int linesPerProcess = numSeqs / processors ;
for (int i = 0; i < closest.size(); i++) {
- cout << querySeqs[i]->getName() << ": ";
+ //cout << querySeqs[i]->getName() << ": ";
+ string file = querySeqs[i]->getName() + ".input";
+ ofstream o;
+ openOutputFile(file, o);
+
+ querySeqs[i]->printSequence(o);
for (int j = 0; j < closest[i].size(); j++) {
-
- cout << closest[i][j]->getName() << '\t';
+ //cout << closest[i][j].seq->getName() << '\t';
+ closest[i][j].seq->printSequence(o);
}
- cout << endl;
+ //cout << endl;
+ o.close();
}
-
+ for (int j = 0; j < numSeqs; j++) {
+ for (int i = 0; i < querySeqs[0]->getAligned().length(); i++) {
+ spotMap[j][i] = i;
+ }
+ }
+
//mask sequences if the user wants to
if (seqMask != "") {
//mask querys
for (int i = 0; i < templateSeqs.size(); i++) {
decalc->runMask(templateSeqs[i]);
}
+
+ for (int i = 0; i < numSeqs; i++) {
+ spotMap[i] = decalc->getMaskMap();
+ }
}
if (filter) {
runFilter(querySeqs);
runFilter(templateSeqs);
+
+ //update spotMap
+ map<int, int> newMap;
+ int spot = 0;
+ int j = 0;
+
+ for (int i = 0; i < filterString.length(); i++) {
+ if (filterString[i] == 1) {
+ //add to newMap
+ newMap[spot] = spotMap[j][i];
+ spot++;
+ }
+ }
+
+ for (int i = 0; i < numSeqs; i++) {
+ spotMap[i] = newMap;
+ }
}
//trim sequences - this follows ccodes remove_extra_gaps
- //just need to pass it query and template since closest points to template
- trimSequences();
+ for (int i = 0; i < querySeqs.size(); i++) {
+ trimSequences(i);
+ }
//windows are equivalent to words - ccode paper recommends windows are between 5% and 20% on alignment length().
//Our default will be 10% and we will warn if user tries to use a window above or below these recommendations
- windows = findWindows();
-
- //remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later
+ for (int i = 0; i < querySeqs.size(); i++) {
+ windows[i] = findWindows(i);
+ }
+
+ //remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later - should be paralellized
for (int i = 0; i < closest.size(); i++) {
removeBadReferenceSeqs(closest[i], i);
}
-
-
+
+
+ //find the averages for each querys references - should be paralellized
+ for (int i = 0; i < numSeqs; i++) {
+ getAverageRef(closest[i], i); //fills sumRef[i], averageRef[i], sumSquaredRef[i] and refCombo[i].
+ }
+
+ //find the averages for the query - should be paralellized
+ for (int i = 0; i < numSeqs; i++) {
+ getAverageQuery(closest[i], i); //fills sumQuery[i], averageQuery[i], sumSquaredQuery[i].
+ }
+
+ //find the averages for each querys references - should be paralellized
+ for (int i = 0; i < numSeqs; i++) {
+ findVarianceRef(i); //fills varRef[i] and sdRef[i] also sets minimum error rate to 0.001 to avoid divide by 0.
+ }
+
+ //find the averages for the query - should be paralellized
+ for (int i = 0; i < numSeqs; i++) {
+ findVarianceQuery(i); //fills varQuery[i] and sdQuery[i] also sets minimum error rate to 0.001 to avoid divide by 0.
+ }
+
+ for (int i = 0; i < numSeqs; i++) {
+ determineChimeras(i); //fills anova, isChimericConfidence[i], isChimericTStudent[i] and isChimericANOVA[i]. - should be paralellized
+ }
+
//free memory
for (int i = 0; i < lines.size(); i++) { delete lines[i]; }
for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i]; }
}
/***************************************************************************************************************/
//ccode algo says it does this to "Removes the initial and final gaps to avoid biases due to incomplete sequences."
-void Ccode::trimSequences() {
+void Ccode::trimSequences(int query) {
try {
int frontPos = 0; //should contain first position in all seqs that is not a gap character
- int rearPos = querySeqs[0]->getAligned().length();
+ int rearPos = querySeqs[query]->getAligned().length();
- //********find first position in all seqs that is a non gap character***********//
+ //********find first position in closest seqs that is a non gap character***********//
//find first position all query seqs that is a non gap character
- for (int i = 0; i < querySeqs.size(); i++) {
+ for (int i = 0; i < closest[query].size(); i++) {
- string aligned = querySeqs[i]->getAligned();
+ string aligned = closest[query][i].seq->getAligned();
int pos = 0;
//find first spot in this seq
if (pos > frontPos) { frontPos = pos; }
}
- //find first position all template seqs that is a non gap character
- for (int i = 0; i < templateSeqs.size(); i++) {
-
- string aligned = templateSeqs[i]->getAligned();
- int pos = 0;
+ //find first position all querySeq[query] that is a non gap character
+ string aligned = querySeqs[query]->getAligned();
+ int pos = 0;
- //find first spot in this seq
- for (int j = 0; j < aligned.length(); j++) {
- if (isalpha(aligned[j])) {
- pos = j;
- break;
- }
+ //find first spot in this seq
+ for (int j = 0; j < aligned.length(); j++) {
+ if (isalpha(aligned[j])) {
+ pos = j;
+ break;
}
-
- //save this spot if it is the farthest
- if (pos > frontPos) { frontPos = pos; }
}
-
- //********find last position in all seqs that is a non gap character***********//
- //find last position all query seqs that is a non gap character
- for (int i = 0; i < querySeqs.size(); i++) {
+ //save this spot if it is the farthest
+ if (pos > frontPos) { frontPos = pos; }
+
+
+ //********find last position in closest seqs that is a non gap character***********//
+ for (int i = 0; i < closest[query].size(); i++) {
- string aligned = querySeqs[i]->getAligned();
+ string aligned = closest[query][i].seq->getAligned();
int pos = aligned.length();
//find first spot in this seq
if (pos < rearPos) { rearPos = pos; }
}
- //find last position all template seqs that is a non gap character
- for (int i = 0; i < templateSeqs.size(); i++) {
-
- string aligned = templateSeqs[i]->getAligned();
- int pos = aligned.length();
-
- //find first spot in this seq
- for (int j = aligned.length()-1; j >= 0; j--) {
- if (isalpha(aligned[j])) {
- pos = j;
- break;
- }
+ //find last position all querySeqs[query] that is a non gap character
+ aligned = querySeqs[query]->getAligned();
+ pos = aligned.length();
+
+ //find first spot in this seq
+ for (int j = aligned.length()-1; j >= 0; j--) {
+ if (isalpha(aligned[j])) {
+ pos = j;
+ break;
}
-
- //save this spot if it is the farthest
- if (pos < rearPos) { rearPos = pos; }
}
+
+ //save this spot if it is the farthest
+ if (pos < rearPos) { rearPos = pos; }
//check to make sure that is not whole seq
if ((rearPos - frontPos - 1) <= 0) { mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); mothurOutEndLine(); exit(1); }
- //***********trim all seqs to that position***************//
- for (int i = 0; i < querySeqs.size(); i++) {
-
- string aligned = querySeqs[i]->getAligned();
-
- //between the two points
- aligned = aligned.substr(frontPos, (rearPos-frontPos-1));
-
- querySeqs[i]->setAligned(aligned);
- }
+ map<int, int> tempTrim;
+ tempTrim[frontPos] = rearPos;
- for (int i = 0; i < templateSeqs.size(); i++) {
-
- string aligned = templateSeqs[i]->getAligned();
-
- //between the two points
- aligned = aligned.substr(frontPos, (rearPos-frontPos-1));
-
- templateSeqs[i]->setAligned(aligned);
+ //save trimmed locations
+ trim[query] = tempTrim;
+
+ //update spotMask
+ map<int, int> newMap;
+ int spot = 0;
+
+ for (int i = frontPos; i < rearPos; i++) {
+ //add to newMap
+//cout << query << '\t' << i << '\t' << spotMap[query][i] << endl;
+ newMap[spot] = spotMap[query][i];
+ spot++;
}
-
+
+ //for (it = newMap.begin(); it!=newMap.end(); it++) {
+ //cout << query << '\t' << it->first << '\t' << it->second << endl;
+ //}
+
+ spotMap[query] = newMap;
+
+
}
catch(exception& e) {
errorOut(e, "Ccode", "trimSequences");
}
/***************************************************************************************************************/
-vector<int> Ccode::findWindows() {
+vector<int> Ccode::findWindows(int query) {
try {
vector<int> win;
- int length = querySeqs[0]->getAligned().length();
+ it = trim[query].begin();
+
+ int length = it->second - it->first;
//default is wanted = 10% of total length
- if (window > length) {
+ if (windowSizes[query] > length) {
mothurOut("You have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.");
- window = length / 10;
- }else if (window == 0) { window = length / 10; }
- else if (window > (length / 20)) {
+ windowSizes[query] = length / 10;
+ }else if (windowSizes[query] == 0) { windowSizes[query] = length / 10; }
+ else if (windowSizes[query] > (length / 20)) {
mothurOut("You have selected a window that is larger than 20% of your sequence length. This is not recommended, but I will continue anyway."); mothurOutEndLine();
- }else if (window < (length / 5)) {
+ }else if (windowSizes[query] < (length / 5)) {
mothurOut("You have selected a window that is smaller than 5% of your sequence length. This is not recommended, but I will continue anyway."); mothurOutEndLine();
}
//save starting points of each window
- for (int m = 0; m < (length-window); m+=window) { win.push_back(m); }
+ for (int m = it->first; m < (it->second-windowSizes[query]); m+=windowSizes[query]) { win.push_back(m); }
+
+ //save last window
+ if (win[win.size()-1] < (it->first+length)) {
+ win.push_back(win[win.size()-1]+windowSizes[query]); // ex. string length is 115, window is 25, without this you would get 0, 25, 50, 75
+ } //with this you would get 1,25,50,75,100
+
return win;
//if you are both not gaps
//if (isalpha(seqA[i]) && isalpha(seqA[i])) {
//are you different
- if (seqA[i] != seqB[i]) { numDiff++; }
+ if (seqA[i] != seqB[i]) {
+ int ok; /* ok=1 means equivalent base. Checks for degenerate bases */
+
+ /* the char in base_a and base_b have been checked and they are different */
+ if ((seqA[i] == 'N') && (seqB[i] != '-')) ok = 1;
+ else if ((seqB[i] == 'N') && (seqA[i] != '-')) ok = 1;
+ else if ((seqA[i] == 'Y') && ((seqB[i] == 'C') || (seqB[i] == 'T'))) ok = 1;
+ else if ((seqB[i] == 'Y') && ((seqA[i] == 'C') || (seqA[i] == 'T'))) ok = 1;
+ else if ((seqA[i] == 'R') && ((seqB[i] == 'G') || (seqB[i] == 'A'))) ok = 1;
+ else if ((seqB[i] == 'R') && ((seqA[i] == 'G') || (seqA[i] == 'A'))) ok = 1;
+ else if ((seqA[i] == 'S') && ((seqB[i] == 'C') || (seqB[i] == 'G'))) ok = 1;
+ else if ((seqB[i] == 'S') && ((seqA[i] == 'C') || (seqA[i] == 'G'))) ok = 1;
+ else if ((seqA[i] == 'W') && ((seqB[i] == 'T') || (seqB[i] == 'A'))) ok = 1;
+ else if ((seqB[i] == 'W') && ((seqA[i] == 'T') || (seqA[i] == 'A'))) ok = 1;
+ else if ((seqA[i] == 'M') && ((seqB[i] == 'A') || (seqB[i] == 'C'))) ok = 1;
+ else if ((seqB[i] == 'M') && ((seqA[i] == 'A') || (seqA[i] == 'C'))) ok = 1;
+ else if ((seqA[i] == 'K') && ((seqB[i] == 'T') || (seqB[i] == 'G'))) ok = 1;
+ else if ((seqB[i] == 'K') && ((seqA[i] == 'T') || (seqA[i] == 'G'))) ok = 1;
+ else if ((seqA[i] == 'V') && ((seqB[i] == 'C') || (seqB[i] == 'A') || (seqB[i] == 'G'))) ok = 1;
+ else if ((seqB[i] == 'V') && ((seqA[i] == 'C') || (seqA[i] == 'A') || (seqA[i] == 'G'))) ok = 1;
+ else if ((seqA[i] == 'H') && ((seqB[i] == 'T') || (seqB[i] == 'A') || (seqB[i] == 'C'))) ok = 1;
+ else if ((seqB[i] == 'H') && ((seqA[i] == 'T') || (seqA[i] == 'A') || (seqA[i] == 'C'))) ok = 1;
+ else if ((seqA[i] == 'D') && ((seqB[i] == 'T') || (seqB[i] == 'A') || (seqB[i] == 'G'))) ok = 1;
+ else if ((seqB[i] == 'D') && ((seqA[i] == 'T') || (seqA[i] == 'A') || (seqA[i] == 'G'))) ok = 1;
+ else if ((seqA[i] == 'B') && ((seqB[i] == 'C') || (seqB[i] == 'T') || (seqB[i] == 'G'))) ok = 1;
+ else if ((seqB[i] == 'B') && ((seqA[i] == 'C') || (seqA[i] == 'T') || (seqA[i] == 'G'))) ok = 1;
+ else ok = 0; /* the bases are different and not equivalent */
+
+ //check if they are both blanks
+ if ((seqA[i] == '.') && (seqB[i] == '-')) ok = 1;
+ else if ((seqB[i] == '.') && (seqA[i] == '-')) ok = 1;
+
+ if (ok == 0) { numDiff++; }
+ }
//}
}
}
//***************************************************************************************************************
//tried to make this look most like ccode original implementation
-void Ccode::removeBadReferenceSeqs(vector<Sequence*>& seqs, int query) {
+void Ccode::removeBadReferenceSeqs(vector<SeqDist>& seqs, int query) {
try {
vector< vector<int> > numDiffBases;
//initialize to 0
for (int i = 0; i < numDiffBases.size(); i++) { numDiffBases[i].resize(seqs.size(),0); }
- int length = seqs[0]->getAligned().length();
+ it = trim[query].begin();
+ int length = it->second - it->first;
//calc differences from each sequence to everyother seq in the set
for (int i = 0; i < seqs.size(); i++) {
- string seqA = seqs[i]->getAligned();
+ string seqA = seqs[i].seq->getAligned().substr(it->first, length);
//so you don't calc i to j and j to i since they are the same
for (int j = 0; j < i; j++) {
- string seqB = seqs[j]->getAligned();
+ string seqB = seqs[j].seq->getAligned().substr(it->first, length);
//compare strings
int numDiff = getDiff(seqA, seqB);
//initailize remove to 0
vector<int> remove; remove.resize(seqs.size(), 0);
+ float top = ((20*length) / (float) 100);
+ float bottom = ((0.5*length) / (float) 100);
//check each numDiffBases and if any are higher than threshold set remove to 1 so you can remove those seqs from the closest set
for (int i = 0; i < numDiffBases.size(); i++) {
- for (int j = 0; j < numDiffBases[i].size(); j++) {
-
+ for (int j = 0; j < i; j++) {
//are you more than 20% different
- if (numDiffBases[i][j] > ((20*length) / 100)) { remove[j] = 1; }
+ if (numDiffBases[i][j] > top) { remove[j] = 1; }
//are you less than 0.5% different
- if (numDiffBases[i][j] < ((0.5*length) / 100)) { remove[j] = 1; }
+ if (numDiffBases[i][j] < bottom) { remove[j] = 1; }
}
}
//if you have enough then remove bad ones
if (numSeqsLeft >= 3) {
- vector<Sequence*> goodSeqs;
+ vector<SeqDist> goodSeqs;
//remove bad seqs
for (int i = 0; i < remove.size(); i++) {
if (remove[i] == 0) {
}
}
//***************************************************************************************************************
-vector< vector<Sequence*> > Ccode::findClosest(int start, int end, int numWanted) {
+vector< vector<SeqDist> > Ccode::findClosest(int start, int end, int numWanted) {
try{
- vector< vector<Sequence*> > topMatches; topMatches.resize(querySeqs.size());
+ vector< vector<SeqDist> > topMatches; topMatches.resize(querySeqs.size());
float smallestOverall, smallestLeft, smallestRight;
smallestOverall = 1000; smallestLeft = 1000; smallestRight = 1000;
//save the number of top matches wanted
for (int h = 0; h < numWanted; h++) {
- topMatches[j].push_back(distances[h].seq);
+ topMatches[j].push_back(distances[h]);
}
}
}
}
/**************************************************************************************************/
-vector<float> Ccode::getAverageRef(vector<Sequence*> ref) {
+//find the distances from each reference sequence to every other reference sequence for each window for this query
+void Ccode::getAverageRef(vector<SeqDist> ref, int query) {
try {
+
+ vector< vector< vector<int> > > diffs; //diffs[0][1][2] is the number of differences between ref seq 0 and ref seq 1 at window 2.
+
+ //initialize diffs vector
+ diffs.resize(ref.size());
+ for (int i = 0; i < diffs.size(); i++) {
+ diffs[i].resize(ref.size());
+ for (int j = 0; j < diffs[i].size(); j++) {
+ diffs[i][j].resize(windows[query].size(), 0);
+ }
+ }
+
+ it = trim[query].begin();
+
+ //find the distances from each reference sequence to every other reference sequence for each window for this query
+ for (int i = 0; i < ref.size(); i++) {
+
+ string refI = ref[i].seq->getAligned();
+
+ //j<i, so you don't find distances from i to j and then j to i.
+ for (int j = 0; j < i; j++) {
+
+ string refJ = ref[j].seq->getAligned();
+
+ for (int k = 0; k < windows[query].size(); k++) {
+
+ string refIWindowk, refJWindowk;
+
+ if (k < windows[query].size()-1) {
+ //get window strings
+ refIWindowk = refI.substr(windows[query][k], windowSizes[query]);
+ refJWindowk = refJ.substr(windows[query][k], windowSizes[query]);
+ }else { //last window may be smaller than rest - see findwindows
+ //get window strings
+ refIWindowk = refI.substr(windows[query][k], (it->second-windows[query][k]));
+ refJWindowk = refJ.substr(windows[query][k], (it->second-windows[query][k]));
+ }
+
+ //find differences
+ int diff = getDiff(refIWindowk, refJWindowk);
+//cout << i << '\t' << j << '\t' << k << '\t' << diff << endl;
+ //save differences in [i][j][k] and [j][i][k] since they are the same
+ diffs[i][j][k] = diff;
+ diffs[j][i][k] = diff;
+
+ }//k
+
+ }//j
+
+ }//i
+
+ //initialize sumRef for this query
+ sumRef[query].resize(windows[query].size(), 0);
+ sumSquaredRef[query].resize(windows[query].size(), 0);
+ averageRef[query].resize(windows[query].size(), 0);
+
+ //find the sum of the differences for hte reference sequences
+ for (int i = 0; i < diffs.size(); i++) {
+ for (int j = 0; j < i; j++) {
+
+ //increment this querys reference sequences combos
+ refCombo[query]++;
+
+ for (int k = 0; k < diffs[i][j].size(); k++) {
+ sumRef[query][k] += diffs[i][j][k];
+ sumSquaredRef[query][k] += (diffs[i][j][k]*diffs[i][j][k]);
+ }//k
+
+ }//j
+ }//i
+
+
+ //find the average of the differences for the references for each window
+ for (int i = 0; i < windows[query].size(); i++) {
+ averageRef[query][i] = sumRef[query][i] / (float) refCombo[query];
+ }
+
}
catch(exception& e) {
errorOut(e, "Ccode", "getAverageRef");
}
}
/**************************************************************************************************/
-vector<float> Ccode::getAverageQuery (vector<Sequence*> ref, int query) {
+void Ccode::getAverageQuery (vector<SeqDist> ref, int query) {
try {
+ vector< vector<int> > diffs; //diffs[1][2] is the number of differences between querySeqs[query] and ref seq 1 at window 2.
+
+ //initialize diffs vector
+ diffs.resize(ref.size());
+ for (int j = 0; j < diffs.size(); j++) {
+ diffs[j].resize(windows[query].size(), 0);
+ }
+
+ it = trim[query].begin();
+
+ string refQuery = querySeqs[query]->getAligned();
+
+ //j<i, so you don't find distances from i to j and then j to i.
+ for (int j = 0; j < ref.size(); j++) {
+
+ string refJ = ref[j].seq->getAligned();
+
+ for (int k = 0; k < windows[query].size(); k++) {
+
+ string QueryWindowk, refJWindowk;
+
+ if (k < windows[query].size()-1) {
+ //get window strings
+ QueryWindowk = refQuery.substr(windows[query][k], windowSizes[query]);
+ refJWindowk = refJ.substr(windows[query][k], windowSizes[query]);
+ }else { //last window may be smaller than rest - see findwindows
+ //get window strings
+ QueryWindowk = refQuery.substr(windows[query][k], (it->second-windows[query][k]));
+ refJWindowk = refJ.substr(windows[query][k], (it->second-windows[query][k]));
+ }
+
+ //find differences
+ int diff = getDiff(QueryWindowk, refJWindowk);
+//cout << j << '\t' << k << '\t' << diff << endl;
+ //save differences
+ diffs[j][k] = diff;
+
+ }//k
+ }//j
+
+
+ //initialize sumRef for this query
+ sumQuery[query].resize(windows[query].size(), 0);
+ sumSquaredQuery[query].resize(windows[query].size(), 0);
+ averageQuery[query].resize(windows[query].size(), 0);
+
+ //find the sum of the differences
+ for (int j = 0; j < diffs.size(); j++) {
+ for (int k = 0; k < diffs[j].size(); k++) {
+ sumQuery[query][k] += diffs[j][k];
+ sumSquaredQuery[query][k] += (diffs[j][k]*diffs[j][k]);
+ }//k
+ }//j
+
+
+ //find the average of the differences for the references for each window
+ for (int i = 0; i < windows[query].size(); i++) {
+ averageQuery[query][i] = sumQuery[query][i] / (float) ref.size();
+ }
+
}
catch(exception& e) {
exit(1);
}
}
+/**************************************************************************************************/
+void Ccode::findVarianceRef (int query) {
+ try {
+
+ varRef[query].resize(windows[query].size(), 0);
+ sdRef[query].resize(windows[query].size(), 0);
+
+ //for each window
+ for (int i = 0; i < windows[query].size(); i++) {
+ varRef[query][i] = (sumSquaredRef[query][i] - ((sumRef[query][i]*sumRef[query][i])/(float)refCombo[query])) / (float)(refCombo[query]-1);
+ sdRef[query][i] = sqrt(varRef[query][i]);
+
+ //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation
+ if (averageRef[query][i] < 0.001) { averageRef[query][i] = 0.001; }
+ if (sumRef[query][i] < 0.001) { sumRef[query][i] = 0.001; }
+ if (varRef[query][i] < 0.001) { varRef[query][i] = 0.001; }
+ if (sumSquaredRef[query][i] < 0.001) { sumSquaredRef[query][i] = 0.001; }
+ if (sdRef[query][i] < 0.001) { sdRef[query][i] = 0.001; }
+
+ }
+ }
+ catch(exception& e) {
+ errorOut(e, "Ccode", "findVarianceRef");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void Ccode::findVarianceQuery (int query) {
+ try {
+ varQuery[query].resize(windows[query].size(), 0);
+ sdQuery[query].resize(windows[query].size(), 0);
+
+ //for each window
+ for (int i = 0; i < windows[query].size(); i++) {
+ varQuery[query][i] = (sumSquaredQuery[query][i] - ((sumQuery[query][i]*sumQuery[query][i])/(float) closest[query].size())) / (float) (closest[query].size()-1);
+ sdQuery[query][i] = sqrt(varQuery[query][i]);
+
+ //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation
+ if (averageQuery[query][i] < 0.001) { averageQuery[query][i] = 0.001; }
+ if (sumQuery[query][i] < 0.001) { sumQuery[query][i] = 0.001; }
+ if (varQuery[query][i] < 0.001) { varQuery[query][i] = 0.001; }
+ if (sumSquaredQuery[query][i] < 0.001) { sumSquaredQuery[query][i] = 0.001; }
+ if (sdQuery[query][i] < 0.001) { sdQuery[query][i] = 0.001; }
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Ccode", "findVarianceQuery");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void Ccode::determineChimeras (int query) {
+ try {
+
+ isChimericConfidence[query].resize(windows[query].size(), false);
+ isChimericTStudent[query].resize(windows[query].size(), false);
+ isChimericANOVA[query].resize(windows[query].size(), false);
+ anova[query].resize(windows[query].size());
+
+
+ //for each window
+ for (int i = 0; i < windows[query].size(); i++) {
+
+ //get confidence limits
+ float t = getT(closest[query].size()-1); //how many seqs you are comparing to this querySeq
+ float dsUpper = (averageQuery[query][i] + (t * sdQuery[query][i])) / averageRef[query][i];
+ float dsLower = (averageQuery[query][i] - (t * sdQuery[query][i])) / averageRef[query][i];
+//cout << t << '\t' << "ds upper = " << dsUpper << " dsLower = " << dsLower << endl;
+ if ((dsUpper > 1.0) && (dsLower > 1.0) && (averageQuery[query][i] > averageRef[query][i])) { /* range does not include 1 */
+ isChimericConfidence[query][i] = true; /* significantly higher at P<0.05 */
+//cout << i << " made it here" << endl;
+ }
+
+ //student t test
+ int degreeOfFreedom = refCombo[query] + closest[query].size() - 2;
+ float denomForT = (((refCombo[query]-1) * varQuery[query][i] + (closest[query].size() - 1) * varRef[query][i]) / (float) degreeOfFreedom) * ((refCombo[query] + closest[query].size()) / (float) (refCombo[query] * closest[query].size())); /* denominator, without sqrt(), for ts calculations */
+
+ float ts = fabs((averageQuery[query][i] - averageRef[query][i]) / (sqrt(denomForT))); /* value of ts for t-student test */
+ t = getT(degreeOfFreedom);
+//cout << i << '\t' << t << '\t' << ts << endl;
+ if ((ts >= t) && (averageQuery[query][i] > averageRef[query][i])) {
+ isChimericTStudent[query][i] = true; /* significantly higher at P<0.05 */
+ }
+
+ //anova test
+ float value1 = sumQuery[query][i] + sumRef[query][i];
+ float value2 = sumSquaredQuery[query][i] + sumSquaredRef[query][i];
+ float value3 = ((sumQuery[query][i]*sumQuery[query][i]) / (float) (closest[query].size())) + ((sumRef[query][i] * sumRef[query][i]) / (float) refCombo[query]);
+ float value4 = (value1 * value1) / ( (float) (closest[query].size() + refCombo[query]) );
+ float value5 = value2 - value4;
+ float value6 = value3 - value4;
+ float value7 = value5 - value6;
+ float value8 = value7 / ((float) degreeOfFreedom);
+ float anovaValue = value6 / value8;
+
+ float f = getF(degreeOfFreedom);
+
+ if ((anovaValue >= f) && (averageQuery[query][i] > averageRef[query][i])) {
+ isChimericANOVA[query][i] = true; /* significant P<0.05 */
+ }
+
+ anova[query][i] = anovaValue;
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Ccode", "determineChimeras");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+float Ccode::getT(int numseq) {
+ try {
+
+ float tvalue = 0;
+
+ /* t-student critical values for different degrees of freedom and alpha 0.1 in one-tail tests (equivalent to 0.05) */
+ if (numseq > 120) tvalue = 1.645;
+ else if (numseq > 60) tvalue = 1.658;
+ else if (numseq > 40) tvalue = 1.671;
+ else if (numseq > 30) tvalue = 1.684;
+ else if (numseq > 29) tvalue = 1.697;
+ else if (numseq > 28) tvalue = 1.699;
+ else if (numseq > 27) tvalue = 1.701;
+ else if (numseq > 26) tvalue = 1.703;
+ else if (numseq > 25) tvalue = 1.706;
+ else if (numseq > 24) tvalue = 1.708;
+ else if (numseq > 23) tvalue = 1.711;
+ else if (numseq > 22) tvalue = 1.714;
+ else if (numseq > 21) tvalue = 1.717;
+ else if (numseq > 20) tvalue = 1.721;
+ else if (numseq > 19) tvalue = 1.725;
+ else if (numseq > 18) tvalue = 1.729;
+ else if (numseq > 17) tvalue = 1.734;
+ else if (numseq > 16) tvalue = 1.740;
+ else if (numseq > 15) tvalue = 1.746;
+ else if (numseq > 14) tvalue = 1.753;
+ else if (numseq > 13) tvalue = 1.761;
+ else if (numseq > 12) tvalue = 1.771;
+ else if (numseq > 11) tvalue = 1.782;
+ else if (numseq > 10) tvalue = 1.796;
+ else if (numseq > 9) tvalue = 1.812;
+ else if (numseq > 8) tvalue = 1.833;
+ else if (numseq > 7) tvalue = 1.860;
+ else if (numseq > 6) tvalue = 1.895;
+ else if (numseq > 5) tvalue = 1.943;
+ else if (numseq > 4) tvalue = 2.015;
+ else if (numseq > 3) tvalue = 2.132;
+ else if (numseq > 2) tvalue = 2.353;
+ else if (numseq > 1) tvalue = 2.920;
+ else if (numseq <= 1) {
+ mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine();
+ }
+
+ return tvalue;
+ }
+ catch(exception& e) {
+ errorOut(e, "Ccode", "getT");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+float Ccode::getF(int numseq) {
+ try {
+
+ float fvalue = 0;
+
+ /* F-Snedecor critical values for v1=1 and different degrees of freedom v2 and alpha 0.05 */
+ if (numseq > 120) fvalue = 3.84;
+ else if (numseq > 60) fvalue = 3.92;
+ else if (numseq > 40) fvalue = 4.00;
+ else if (numseq > 30) fvalue = 4.08;
+ else if (numseq > 29) fvalue = 4.17;
+ else if (numseq > 28) fvalue = 4.18;
+ else if (numseq > 27) fvalue = 4.20;
+ else if (numseq > 26) fvalue = 4.21;
+ else if (numseq > 25) fvalue = 4.23;
+ else if (numseq > 24) fvalue = 4.24;
+ else if (numseq > 23) fvalue = 4.26;
+ else if (numseq > 22) fvalue = 4.28;
+ else if (numseq > 21) fvalue = 4.30;
+ else if (numseq > 20) fvalue = 4.32;
+ else if (numseq > 19) fvalue = 4.35;
+ else if (numseq > 18) fvalue = 4.38;
+ else if (numseq > 17) fvalue = 4.41;
+ else if (numseq > 16) fvalue = 4.45;
+ else if (numseq > 15) fvalue = 4.49;
+ else if (numseq > 14) fvalue = 4.54;
+ else if (numseq > 13) fvalue = 4.60;
+ else if (numseq > 12) fvalue = 4.67;
+ else if (numseq > 11) fvalue = 4.75;
+ else if (numseq > 10) fvalue = 4.84;
+ else if (numseq > 9) fvalue = 4.96;
+ else if (numseq > 8) fvalue = 5.12;
+ else if (numseq > 7) fvalue = 5.32;
+ else if (numseq > 6) fvalue = 5.59;
+ else if (numseq > 5) fvalue = 5.99;
+ else if (numseq > 4) fvalue = 6.61;
+ else if (numseq > 3) fvalue = 7.71;
+ else if (numseq > 2) fvalue = 10.1;
+ else if (numseq > 1) fvalue = 18.5;
+ else if (numseq > 0) fvalue = 161;
+ else if (numseq <= 0) {
+ mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine();
+ }
+
+ return fvalue;
+ }
+ catch(exception& e) {
+ errorOut(e, "Ccode", "getF");
+ exit(1);
+ }
+}
+
/**************************************************************************************************/
void Ccode::createProcessesClosest() {
try {
//output pairs
for (int i = lines[process]->start; i < lines[process]->end; i++) {
for (int j = 0; j < closest[i].size(); j++) {
- closest[i][j]->printSequence(out);
+ closest[i][j].seq->printSequence(out);
}
}
+ out << ">" << endl; //to stop sequence read
+
+ for (int i = lines[process]->start; i < lines[process]->end; i++) {
+ for (int j = 0; j < closest[i].size(); j++) {
+ out << closest[i][j].dist << '\t';
+ }
+ out << endl;
+ }
+
out.close();
exit(0);
string s = toString(processIDS[i]) + ".temp";
openInputFile(s, in);
+ vector< vector<Sequence*> > tempClosest; tempClosest.resize(querySeqs.size());
//get pairs
for (int k = lines[i]->start; k < lines[i]->end; k++) {
-
vector<Sequence*> tempVector;
for (int j = 0; j < numWanted; j++) {
tempVector.push_back(temp);
}
- closest[k] = tempVector;
+ tempClosest[k] = tempVector;
}
+ string junk;
+ in >> junk; gobble(in); // to get ">"
+
+ vector< vector<float> > dists; dists.resize(querySeqs.size());
+
+ for (int i = lines[process]->start; i < lines[process]->end; i++) {
+ dists[i].resize(closest[i].size());
+ for (int j = 0; j < closest[i].size(); j++) {
+ in >> dists[i][j];
+ }
+ gobble(in);
+ }
+
+ for (int i = lines[process]->start; i < lines[process]->end; i++) {
+ for (int j = 0; j < closest[i].size(); j++) {
+ closest[i][j].seq = tempClosest[i][j];
+ closest[i][j].dist = dists[i][j];
+ }
+ }
+
in.close();
remove(s.c_str());
}
projects / mothur.git / commitdiff