--- /dev/null
+/*
+ * ccode.cpp
+ * Mothur
+ *
+ * Created by westcott on 8/24/09.
+ * Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "ccode.h"
+#include "ignoregaps.h"
+#include "eachgapdist.h"
+
+//***************************************************************************************************************
+Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int numW, string o) : Chimera() {
+ try {
+
+ fastafile = filename;
+ outputDir = o;
+ templateFileName = temp; templateSeqs = readSeqs(temp);
+ setMask(mask);
+ filter = f;
+ window = win;
+ numWanted = numW;
+
+ distCalc = new eachGapDist();
+ decalc = new DeCalculator();
+
+ mapInfo = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "mapinfo";
+
+ #ifdef USE_MPI
+
+ //char* inFileName = new char[mapInfo.length()];
+ //memcpy(inFileName, mapInfo.c_str(), mapInfo.length());
+
+ char inFileName[1024];
+ strcpy(inFileName, mapInfo.c_str());
+
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, outMode, MPI_INFO_NULL, &outMap); //comm, filename, mode, info, filepointer
+
+ //delete inFileName;
+
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ if (pid == 0) {
+ string outString = "Place in masked, filtered and trimmed sequence\tPlace in original alignment\n";
+
+ MPI_Status status;
+ int length = outString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outString.c_str(), length);
+
+ MPI_File_write_shared(outMap, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+ }
+ #else
+
+ ofstream out2;
+ m->openOutputFile(mapInfo, out2);
+
+ out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
+ out2.close();
+ #endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "Ccode");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+Ccode::~Ccode() {
+ delete distCalc;
+ delete decalc;
+
+ #ifdef USE_MPI
+ MPI_File_close(&outMap);
+ #endif
+}
+//***************************************************************************************************************
+Sequence Ccode::print(ostream& out, ostream& outAcc) {
+ try {
+
+ ofstream out2;
+ m->openOutputFileAppend(mapInfo, out2);
+
+ out2 << querySeq->getName() << endl;
+ for (it = spotMap.begin(); it!= spotMap.end(); it++) {
+ out2 << it->first << '\t' << it->second << endl;
+ }
+ out2.close();
+ out << querySeq->getName() << endl << endl << "Reference sequences used and distance to query:" << endl;
+
+ for (int j = 0; j < closest.size(); j++) {
+ out << closest[j].seq->getName() << '\t' << closest[j].dist << endl;
+ }
+ out << endl << endl;
+
+ //for each window
+ //window mapping info.
+ out << "Mapping information: ";
+ //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 << endl << "Window\tStartPos\tEndPos" << endl;
+ it = trim.begin();
+ for (int k = 0; k < windows.size()-1; k++) {
+ out << k+1 << '\t' << spotMap[windows[k]-it->first] << '\t' << spotMap[windows[k]-it->first+windowSizes] << endl;
+ }
+
+ out << windows.size() << '\t' << spotMap[windows[windows.size()-1]-it->first] << '\t' << spotMap[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.size(); k++) {
+ float ds = averageQuery[k] / averageRef[k];
+ out << k+1 << '\t' << averageQuery[k] << '\t' << sdQuery[k] << '\t' << averageRef[k] << '\t'<< sdRef[k] << '\t' << ds << '\t' << anova[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] / varRef[query]; /* 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.size(); k++) {
+ string temp = "";
+ if (isChimericConfidence[k]) { temp += "*\t"; }
+ else { temp += "\t"; }
+
+ if (isChimericTStudent[k]) { temp += "*\t"; }
+ else { temp += "\t"; }
+
+ if (isChimericANOVA[k]) { temp += "*\t"; }
+ else { temp += "\t"; }
+
+ out << k+1 << '\t' << temp << endl;
+
+ if (temp == "*\t*\t*\t") { results = true; }
+ }
+ out << endl;
+
+ if (results) {
+ m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
+ outAcc << querySeq->getName() << endl;
+ }
+
+ //free memory
+ for (int i = 0; i < closest.size(); i++) { delete closest[i].seq; }
+
+ return *querySeq;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "print");
+ exit(1);
+ }
+}
+#ifdef USE_MPI
+//***************************************************************************************************************
+Sequence Ccode::print(MPI_File& out, MPI_File& outAcc) {
+ try {
+
+ string outMapString = "";
+
+ outMapString += querySeq->getName() + "\n";
+ for (it = spotMap.begin(); it!= spotMap.end(); it++) {
+ outMapString += toString(it->first) + "\t" + toString(it->second) + "\n";
+ }
+ printMapping(outMapString);
+ outMapString = "";
+
+ string outString = "";
+ string outAccString = "";
+
+ outString += querySeq->getName() + "\n\nReference sequences used and distance to query:\n";
+
+ for (int j = 0; j < closest.size(); j++) {
+ outString += closest[j].seq->getName() + "\t" + toString(closest[j].dist) + "\n";
+ }
+ outString += "\n\nMapping information: ";
+
+ //for each window
+ //window mapping info.
+ //you mask and did not filter
+ if ((seqMask != "") && (!filter)) { outString += "mask and trim."; }
+
+ //you filtered and did not mask
+ if ((seqMask == "") && (filter)) { outString += "filter and trim."; }
+
+ //you masked and filtered
+ if ((seqMask != "") && (filter)) { outString += "mask, filter and trim."; }
+
+ outString += "\nWindow\tStartPos\tEndPos\n";
+ it = trim.begin();
+ for (int k = 0; k < windows.size()-1; k++) {
+ outString += toString(k+1) + "\t" + toString(spotMap[windows[k]-it->first]) + "\t" + toString(spotMap[windows[k]-it->first+windowSizes]) + "\n";
+ }
+
+ outString += toString(windows.size()) + "\t" + toString(spotMap[windows[windows.size()-1]-it->first]) + "\t" + toString(spotMap[it->second-it->first-1]) + "\n\n";
+
+ outString += "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova\n";
+ for (int k = 0; k < windows.size(); k++) {
+ float ds = averageQuery[k] / averageRef[k];
+ outString += toString(k+1) + "\t" + toString(averageQuery[k]) + "\t" + toString(sdQuery[k]) + "\t" + toString(averageRef[k]) + "\t" + toString(sdRef[k]) + "\t" + toString(ds) + "\t" + toString(anova[k]) + "\n";
+ }
+
+ //varRef
+ //varQuery
+ /* F test for differences among variances.
+ * varQuery is expected to be higher or similar than varRef */
+ //float fs = varQuery[query] / varRef[query]; /* F-Snedecor, test for differences of variances */
+
+ bool results = false;
+
+ //confidence limit, t - Student, anova
+ outString += "\nWindow\tConfidenceLimit\tt-Student\tAnova\n";
+
+ for (int k = 0; k < windows.size(); k++) {
+ string temp = "";
+ if (isChimericConfidence[k]) { temp += "*\t"; }
+ else { temp += "\t"; }
+
+ if (isChimericTStudent[k]) { temp += "*\t"; }
+ else { temp += "\t"; }
+
+ if (isChimericANOVA[k]) { temp += "*\t"; }
+ else { temp += "\t"; }
+
+ outString += toString(k+1) + "\t" + temp + "\n";
+
+ if (temp == "*\t*\t*\t") { results = true; }
+ }
+ outString += "\n";
+
+ MPI_Status status;
+ int length = outString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outString.c_str(), length);
+
+ MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+
+ if (results) {
+ m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
+ outAccString += querySeq->getName() + "\n";
+
+ MPI_Status statusAcc;
+ length = outAccString.length();
+ char* buf = new char[length];
+ memcpy(buf, outAccString.c_str(), length);
+
+ MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
+ delete buf;
+ }
+
+ //free memory
+ for (int i = 0; i < closest.size(); i++) { delete closest[i].seq; }
+
+ return *querySeq;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "print");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int Ccode::printMapping(string& output) {
+ try {
+ MPI_Status status;
+ int length = output.length();
+ char* buf = new char[length];
+ memcpy(buf, output.c_str(), length);
+
+ MPI_File_write_shared(outMap, buf, length, MPI_CHAR, &status);
+ delete buf;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "printMapping");
+ exit(1);
+ }
+}
+#endif
+//***************************************************************************************************************
+int Ccode::getChimeras(Sequence* query) {
+ try {
+
+ closest.clear();
+ refCombo = 0;
+ sumRef.clear();
+ varRef.clear();
+ varQuery.clear();
+ sdRef.clear();
+ sdQuery.clear();
+ sumQuery.clear();
+ sumSquaredRef.clear();
+ sumSquaredQuery.clear();
+ averageRef.clear();
+ averageQuery.clear();
+ anova.clear();
+ isChimericConfidence.clear();
+ isChimericTStudent.clear();
+ isChimericANOVA.clear();
+ trim.clear();
+ spotMap.clear();
+ windowSizes = window;
+ windows.clear();
+
+
+ querySeq = query;
+
+ //find closest matches to query
+ closest = findClosest(query, numWanted);
+
+ if (m->control_pressed) { return 0; }
+
+ //initialize spotMap
+ for (int i = 0; i < query->getAligned().length(); i++) { spotMap[i] = i; }
+
+ //mask sequences if the user wants to
+ if (seqMask != "") {
+ decalc->setMask(seqMask);
+
+ decalc->runMask(query);
+
+ //mask closest
+ for (int i = 0; i < closest.size(); i++) { decalc->runMask(closest[i].seq); }
+
+ spotMap = decalc->getMaskMap();
+ }
+
+ if (filter) {
+ vector<Sequence*> temp;
+ for (int i = 0; i < closest.size(); i++) { temp.push_back(closest[i].seq); }
+ temp.push_back(query);
+
+ createFilter(temp, 0.5);
+
+ for (int i = 0; i < temp.size(); i++) {
+ if (m->control_pressed) { return 0; }
+ runFilter(temp[i]);
+ }
+
+ //update spotMap
+ map<int, int> newMap;
+ int spot = 0;
+
+ for (int i = 0; i < filterString.length(); i++) {
+ if (filterString[i] == '1') {
+ //add to newMap
+ newMap[spot] = spotMap[i];
+ spot++;
+ }
+ }
+ spotMap = newMap;
+ }
+
+ //trim sequences - this follows ccodes remove_extra_gaps
+ trimSequences(query);
+ if (m->control_pressed) { return 0; }
+
+ //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();
+ if (m->control_pressed) { return 0; }
+
+ //remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later
+ removeBadReferenceSeqs(closest);
+ if (m->control_pressed) { return 0; }
+
+ //find the averages for each querys references
+ getAverageRef(closest); //fills sumRef, averageRef, sumSquaredRef and refCombo.
+ getAverageQuery(closest, query); //fills sumQuery, averageQuery, sumSquaredQuery.
+ if (m->control_pressed) { return 0; }
+
+ //find the averages for each querys references
+ findVarianceRef(); //fills varRef and sdRef also sets minimum error rate to 0.001 to avoid divide by 0.
+ if (m->control_pressed) { return 0; }
+
+ //find the averages for the query
+ findVarianceQuery(); //fills varQuery and sdQuery also sets minimum error rate to 0.001 to avoid divide by 0.
+ if (m->control_pressed) { return 0; }
+
+ determineChimeras(); //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA.
+ if (m->control_pressed) { return 0; }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "getChimeras");
+ exit(1);
+ }
+}
+/***************************************************************************************************************/
+//ccode algo says it does this to "Removes the initial and final gaps to avoid biases due to incomplete sequences."
+void Ccode::trimSequences(Sequence* query) {
+ try {
+
+ int frontPos = 0; //should contain first position in all seqs that is not a gap character
+ int rearPos = query->getAligned().length();
+
+ //********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 < closest.size(); i++) {
+
+ string aligned = closest[i].seq->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;
+ }
+ }
+
+ //save this spot if it is the farthest
+ if (pos > frontPos) { frontPos = pos; }
+ }
+
+ //find first position all querySeq[query] that is a non gap character
+ string aligned = 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;
+ }
+ }
+
+ //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.size(); i++) {
+
+ string aligned = closest[i].seq->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;
+ }
+ }
+
+ //save this spot if it is the farthest
+ if (pos < rearPos) { rearPos = pos; }
+ }
+
+ //find last position all querySeqs[query] that is a non gap character
+ aligned = 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; }
+
+
+ //check to make sure that is not whole seq
+ if ((rearPos - frontPos - 1) <= 0) { m->mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine(); exit(1); }
+
+ map<int, int> tempTrim;
+ tempTrim[frontPos] = rearPos;
+
+ //save trimmed locations
+ trim = tempTrim;
+
+ //update spotMask
+ map<int, int> newMap;
+ int spot = 0;
+
+ for (int i = frontPos; i < rearPos; i++) {
+ //add to newMap
+ newMap[spot] = spotMap[i];
+ spot++;
+ }
+ spotMap = newMap;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "trimSequences");
+ exit(1);
+ }
+}
+/***************************************************************************************************************/
+vector<int> Ccode::findWindows() {
+ try {
+
+ vector<int> win;
+ it = trim.begin();
+
+ int length = it->second - it->first;
+
+ //default is wanted = 10% of total length
+ if (windowSizes > length) {
+ m->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.");
+ windowSizes = length / 10;
+ }else if (windowSizes == 0) { windowSizes = length / 10; }
+ else if (windowSizes > (length * 0.20)) {
+ m->mothurOut("You have selected a window that is larger than 20% of your sequence length. This is not recommended, but I will continue anyway."); m->mothurOutEndLine();
+ }else if (windowSizes < (length * 0.05)) {
+ m->mothurOut("You have selected a window that is smaller than 5% of your sequence length. This is not recommended, but I will continue anyway."); m->mothurOutEndLine();
+ }
+
+ //save starting points of each window
+ for (int m = it->first; m < (it->second-windowSizes); m+=windowSizes) { win.push_back(m); }
+
+ //save last window
+ if (win[win.size()-1] < (it->first+length)) {
+ win.push_back(win[win.size()-1]+windowSizes); // 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;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "findWindows");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int Ccode::getDiff(string seqA, string seqB) {
+ try {
+
+ int numDiff = 0;
+
+ for (int i = 0; i < seqA.length(); i++) {
+ //if you are both not gaps
+ //if (isalpha(seqA[i]) && isalpha(seqA[i])) {
+ //are you different
+ 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++; }
+ }
+ //}
+ }
+
+ return numDiff;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "getDiff");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+//tried to make this look most like ccode original implementation
+void Ccode::removeBadReferenceSeqs(vector<SeqDist>& seqs) {
+ try {
+
+ vector< vector<int> > numDiffBases;
+ numDiffBases.resize(seqs.size());
+ //initialize to 0
+ for (int i = 0; i < numDiffBases.size(); i++) { numDiffBases[i].resize(seqs.size(),0); }
+
+ it = trim.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].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].seq->getAligned().substr(it->first, length);
+
+ //compare strings
+ int numDiff = getDiff(seqA, seqB);
+
+ numDiffBases[i][j] = numDiff;
+ numDiffBases[j][i] = numDiff;
+ }
+ }
+
+ //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 < i; j++) {
+ //are you more than 20% different
+ if (numDiffBases[i][j] > top) { remove[j] = 1; }
+ //are you less than 0.5% different
+ if (numDiffBases[i][j] < bottom) { remove[j] = 1; }
+ }
+ }
+
+ int numSeqsLeft = 0;
+
+ //count seqs that are not going to be removed
+ for (int i = 0; i < remove.size(); i++) {
+ if (remove[i] == 0) { numSeqsLeft++; }
+ }
+
+ //if you have enough then remove bad ones
+ if (numSeqsLeft >= 3) {
+ vector<SeqDist> goodSeqs;
+ //remove bad seqs
+ for (int i = 0; i < remove.size(); i++) {
+ if (remove[i] == 0) {
+ goodSeqs.push_back(seqs[i]);
+ }
+ }
+
+ seqs = goodSeqs;
+
+ }else { //warn, but dont remove any
+ m->mothurOut(querySeq->getName() + " does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check."); m->mothurOutEndLine();
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "removeBadReferenceSeqs");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+//makes copy of templateseq for filter
+vector<SeqDist> Ccode::findClosest(Sequence* q, int numWanted) {
+ try{
+
+ vector<SeqDist> topMatches;
+
+ Sequence query = *(q);
+
+ //calc distance to each sequence in template seqs
+ for (int i = 0; i < templateSeqs.size(); i++) {
+
+ Sequence ref = *(templateSeqs[i]);
+
+ //find overall dist
+ distCalc->calcDist(query, ref);
+ float dist = distCalc->getDist();
+
+ //save distance
+ SeqDist temp;
+ temp.seq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
+ temp.dist = dist;
+
+ topMatches.push_back(temp);
+ }
+
+ sort(topMatches.begin(), topMatches.end(), compareSeqDist);
+
+ for (int i = numWanted; i < topMatches.size(); i++) { delete topMatches[i].seq; }
+
+ topMatches.resize(numWanted);
+
+ return topMatches;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "findClosestSides");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+//find the distances from each reference sequence to every other reference sequence for each window for this query
+void Ccode::getAverageRef(vector<SeqDist> ref) {
+ 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.size(), 0);
+ }
+ }
+
+ it = trim.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.size(); k++) {
+
+ string refIWindowk, refJWindowk;
+
+ if (k < windows.size()-1) {
+ //get window strings
+ refIWindowk = refI.substr(windows[k], windowSizes);
+ refJWindowk = refJ.substr(windows[k], windowSizes);
+ }else { //last window may be smaller than rest - see findwindows
+ //get window strings
+ refIWindowk = refI.substr(windows[k], (it->second-windows[k]));
+ refJWindowk = refJ.substr(windows[k], (it->second-windows[k]));
+ }
+
+ //find differences
+ int diff = getDiff(refIWindowk, refJWindowk);
+
+ //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.resize(windows.size(), 0);
+ sumSquaredRef.resize(windows.size(), 0);
+ averageRef.resize(windows.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++;
+
+ for (int k = 0; k < diffs[i][j].size(); k++) {
+ sumRef[k] += diffs[i][j][k];
+ sumSquaredRef[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.size(); i++) {
+ averageRef[i] = sumRef[i] / (float) refCombo;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "getAverageRef");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void Ccode::getAverageQuery (vector<SeqDist> ref, Sequence* 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.size(), 0);
+ }
+
+ it = trim.begin();
+
+ string refQuery = 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.size(); k++) {
+
+ string QueryWindowk, refJWindowk;
+
+ if (k < windows.size()-1) {
+ //get window strings
+ QueryWindowk = refQuery.substr(windows[k], windowSizes);
+ refJWindowk = refJ.substr(windows[k], windowSizes);
+ }else { //last window may be smaller than rest - see findwindows
+ //get window strings
+ QueryWindowk = refQuery.substr(windows[k], (it->second-windows[k]));
+ refJWindowk = refJ.substr(windows[k], (it->second-windows[k]));
+ }
+
+ //find differences
+ int diff = getDiff(QueryWindowk, refJWindowk);
+
+ //save differences
+ diffs[j][k] = diff;
+
+ }//k
+ }//j
+
+
+ //initialize sumRef for this query
+ sumQuery.resize(windows.size(), 0);
+ sumSquaredQuery.resize(windows.size(), 0);
+ averageQuery.resize(windows.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[k] += diffs[j][k];
+ sumSquaredQuery[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.size(); i++) {
+ averageQuery[i] = sumQuery[i] / (float) ref.size();
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "getAverageQuery");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void Ccode::findVarianceRef() {
+ try {
+
+ varRef.resize(windows.size(), 0);
+ sdRef.resize(windows.size(), 0);
+
+ //for each window
+ for (int i = 0; i < windows.size(); i++) {
+ varRef[i] = (sumSquaredRef[i] - ((sumRef[i]*sumRef[i])/(float)refCombo)) / (float)(refCombo-1);
+ sdRef[i] = sqrt(varRef[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[i] < 0.001) { averageRef[i] = 0.001; }
+ if (sumRef[i] < 0.001) { sumRef[i] = 0.001; }
+ if (varRef[i] < 0.001) { varRef[i] = 0.001; }
+ if (sumSquaredRef[i] < 0.001) { sumSquaredRef[i] = 0.001; }
+ if (sdRef[i] < 0.001) { sdRef[i] = 0.001; }
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "findVarianceRef");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void Ccode::findVarianceQuery() {
+ try {
+ varQuery.resize(windows.size(), 0);
+ sdQuery.resize(windows.size(), 0);
+
+ //for each window
+ for (int i = 0; i < windows.size(); i++) {
+ varQuery[i] = (sumSquaredQuery[i] - ((sumQuery[i]*sumQuery[i])/(float) closest.size())) / (float) (closest.size()-1);
+ sdQuery[i] = sqrt(varQuery[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[i] < 0.001) { averageQuery[i] = 0.001; }
+ if (sumQuery[i] < 0.001) { sumQuery[i] = 0.001; }
+ if (varQuery[i] < 0.001) { varQuery[i] = 0.001; }
+ if (sumSquaredQuery[i] < 0.001) { sumSquaredQuery[i] = 0.001; }
+ if (sdQuery[i] < 0.001) { sdQuery[i] = 0.001; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "findVarianceQuery");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void Ccode::determineChimeras() {
+ try {
+
+ isChimericConfidence.resize(windows.size(), false);
+ isChimericTStudent.resize(windows.size(), false);
+ isChimericANOVA.resize(windows.size(), false);
+ anova.resize(windows.size());
+
+
+ //for each window
+ for (int i = 0; i < windows.size(); i++) {
+
+ //get confidence limits
+ float t = getT(closest.size()-1); //how many seqs you are comparing to this querySeq
+ float dsUpper = (averageQuery[i] + (t * sdQuery[i])) / averageRef[i];
+ float dsLower = (averageQuery[i] - (t * sdQuery[i])) / averageRef[i];
+
+ if ((dsUpper > 1.0) && (dsLower > 1.0) && (averageQuery[i] > averageRef[i])) { /* range does not include 1 */
+ isChimericConfidence[i] = true; /* significantly higher at P<0.05 */
+
+ }
+
+ //student t test
+ int degreeOfFreedom = refCombo + closest.size() - 2;
+ float denomForT = (((refCombo-1) * varQuery[i] + (closest.size() - 1) * varRef[i]) / (float) degreeOfFreedom) * ((refCombo + closest.size()) / (float) (refCombo * closest.size())); /* denominator, without sqrt(), for ts calculations */
+
+ float ts = fabs((averageQuery[i] - averageRef[i]) / (sqrt(denomForT))); /* value of ts for t-student test */
+ t = getT(degreeOfFreedom);
+
+ if ((ts >= t) && (averageQuery[i] > averageRef[i])) {
+ isChimericTStudent[i] = true; /* significantly higher at P<0.05 */
+ }
+
+ //anova test
+ float value1 = sumQuery[i] + sumRef[i];
+ float value2 = sumSquaredQuery[i] + sumSquaredRef[i];
+ float value3 = ((sumQuery[i]*sumQuery[i]) / (float) (closest.size())) + ((sumRef[i] * sumRef[i]) / (float) refCombo);
+ float value4 = (value1 * value1) / ( (float) (closest.size() + refCombo) );
+ 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[i] > averageRef[i])) {
+ isChimericANOVA[i] = true; /* significant P<0.05 */
+ }
+
+ if (isnan(anovaValue) || isinf(anovaValue)) { anovaValue = 0.0; }
+
+ anova[i] = anovaValue;
+ }
+
+ }
+ catch(exception& e) {
+ m->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) {
+ m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
+ }
+
+ return tvalue;
+ }
+ catch(exception& e) {
+ m->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) {
+ m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
+ }
+
+ return fvalue;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Ccode", "getF");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+
+
projects / mothur.git / blobdiff