try {
for (int i = 0; i < querySeqs.size(); i++) { delete querySeqs[i]; }
for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; }
-
- if (processors != 1) { for (int i = 0; i < bestfit.size(); i++) { delete bestfit[i]; } }
+ for (int i = 0; i < bestfit.size(); i++) { delete bestfit[i]; }
}
catch(exception& e) {
errorOut(e, "Pintail", "~Pintail");
void Pintail::print(ostream& out) {
try {
+ mothurOutEndLine();
+
for (int i = 0; i < querySeqs.size(); i++) {
int index = ceil(deviation[i]);
-float quan = 2.64 * log10(deviation[i]) + 1.46;
-cout << "dist = " << index << endl;
-cout << "de = " << DE[i] << endl;
-cout << "mallard quantile = " << quan << endl;
-cout << "my quantile = " << quantiles[index][4] << endl;
//is your DE value higher than the 95%
string chimera;
- if (DE[i] > quantiles[index][4]) { chimera = "Yes"; }
- else { chimera = "No"; }
+ if (DE[i] > quantiles[index][4]) { chimera = "Yes"; }
+ else { chimera = "No"; }
out << querySeqs[i]->getName() << '\t' << "div: " << deviation[i] << "\tstDev: " << DE[i] << "\tchimera flag: " << chimera << endl;
if (chimera == "Yes") {
windowsForeachQuery.resize(numSeqs);
h.resize(numSeqs);
quantiles.resize(100); //one for every percent mismatch
+ quantilesMembers.resize(100); //one for every percent mismatch
+ makeCompliant.resize(templateSeqs.size(), 0.0);
//break up file if needed
int linesPerProcess = numSeqs / processors ;
distcalculator = new ignoreGaps();
decalc = new DeCalculator();
+ //if the user does enter a mask then you want to keep all the spots in the alignment
+ if (seqMask.length() == 0) { decalc->setAlignmentLength(querySeqs[0]->getAligned().length()); }
+ else { decalc->setAlignmentLength(seqMask.length()); }
+
decalc->setMask(seqMask);
//find pairs
}else { createProcessesPairs(); }
- for (int j = 0; j < bestfit.size(); j++) {
- //chops off beginning and end of sequences so they both start and end with a base
- ofstream out;
- string s = querySeqs[j]->getName();
-
- openOutputFile(s, out);
- out << ">" << querySeqs[j]->getName() << endl;
- out << querySeqs[j]->getAligned() << endl;
- out.close();
-
- string t =querySeqs[j]->getName() + ".ref";
- openOutputFile(t, out);
- out << ">" << bestfit[j]->getName() << endl;
- out << bestfit[j]->getAligned() << endl;
- out.close();
- }
-
-
//find P
mothurOut("Getting conservation... "); cout.flush();
if (consfile == "") {
}else { probabilityProfile = readFreq(); }
//make P into Q
- for (int i = 0; i < probabilityProfile.size(); i++) { probabilityProfile[i] = 1 - probabilityProfile[i]; } //cout << i << '\t' << probabilityProfile[i] << endl;
+ for (int i = 0; i < probabilityProfile.size(); i++) { probabilityProfile[i] = 1 - probabilityProfile[i]; } //cout << i << '\t' << probabilityProfile[i] << endl;
mothurOut("Done."); mothurOutEndLine();
- //mask querys
- for (int i = 0; i < querySeqs.size(); i++) {
- //cout << querySeqs[i]->getName() << " before mask = " << querySeqs[i]->getAligned() << endl << endl;
- decalc->runMask(querySeqs[i]);
- //cout << querySeqs[i]->getName() << " after mask = " << querySeqs[i]->getAligned() << endl << endl;
- }
+ //mask sequences if the user wants to
+ if (seqMask != "") {
+ //mask querys
+ for (int i = 0; i < querySeqs.size(); i++) {
+ decalc->runMask(querySeqs[i]);
+ }
- //mask templates
- for (int i = 0; i < templateSeqs.size(); i++) {
- decalc->runMask(templateSeqs[i]);
+ //mask templates
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ decalc->runMask(templateSeqs[i]);
+ }
+
+ for (int i = 0; i < bestfit.size(); i++) {
+ decalc->runMask(bestfit[i]);
+ }
+
}
-
-//for (int i = 0; i < lines.size(); i++) { cout << "line pair " << i << " = " << lines[i]->start << '\t' << lines[i]->end << endl; }
-
+
if (processors == 1) {
for (int j = 0; j < bestfit.size(); j++) {
- cout << querySeqs[j]->getName() << " after mask = " << querySeqs[j]->getAligned() << endl << endl;
- cout << bestfit[j]->getName() << " after mask = " << bestfit[j]->getAligned() << endl << endl;
decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]);
}
mothurOut("Finding window breaks... "); cout.flush();
for (int i = lines[0]->start; i < lines[0]->end; i++) {
it = trimmed[i].begin();
-cout << i << '\t' << "trimmed = " << it->first << '\t' << it->second << endl;
vector<int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
windowsForeachQuery[i] = win;
}
mothurOut("Done."); mothurOutEndLine();
}else { createProcessesSpots(); }
-
if (processors == 1) {
mothurOut("Calculating observed distance... "); cout.flush();
for (int i = lines[0]->start; i < lines[0]->end; i++) {
- cout << querySeqs[i]->getName() << '\t' << bestfit[i]->getName() << " windows = " << windowsForeachQuery[i].size() << " size = " << windowSizes[i] << endl;
vector<float> obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
- for (int j = 0; j < obsi.size(); j++) {
- cout << obsi[j] << '\t';
- }
- cout << endl;
obsDistance[i] = obsi;
}
mothurOut("Done."); mothurOutEndLine();
vector<float> q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile);
Qav[i] = q;
-cout << i+1 << endl;
-for (int j = 0; j < Qav[i].size(); j++) {
- cout << Qav[i][j] << '\t';
-}
-cout << endl << endl;
-
}
mothurOut("Done."); mothurOutEndLine();
mothurOut("Calculating alpha... "); cout.flush();
for (int i = lines[0]->start; i < lines[0]->end; i++) {
float alpha = decalc->getCoef(obsDistance[i], Qav[i]);
-cout << i+1 << "\tcoef = " << alpha << endl;
seqCoef[i] = alpha;
}
mothurOut("Done."); mothurOutEndLine();
for (int i = lines[0]->start; i < lines[0]->end; i++) {
float de = decalc->calcDE(obsDistance[i], expectedDistance[i]);
DE[i] = de;
-cout << querySeqs[i]->getName() << '\t' << "de value = " << de << endl;
+
it = trimmed[i].begin();
float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second);
-cout << querySeqs[i]->getName() << '\t' << "dist value = " << dist << endl;
deviation[i] = dist;
}
mothurOut("Done."); mothurOutEndLine();
}
else { createProcesses(); }
-
//quantiles are used to determine whether the de values found indicate a chimera
//if you have to calculate them, its time intensive because you are finding the de and deviation values for each
//combination of sequences in the template
mothurOut("Calculating quantiles for your template. This can take a while... I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command. Providing the .quan file will dramatically improve speed. "); cout.flush();
if (processors == 1) {
- quantiles = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
+ quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size(), makeCompliant);
}else { createProcessesQuan(); }
-
- decalc->removeObviousOutliers(quantiles);
+
+ //decided against this because we were having trouble setting the sensitivity... may want to revisit this...
+ //quantiles = decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
ofstream out4;
- string o = getRootName(templateFile) + "quan";
+ string o;
+
+ o = getRootName(templateFile) + "quan";
openOutputFile(o, out4);
//adjust quantiles
for (int i = 0; i < quantiles.size(); i++) {
+ vector<float> temp;
+
if (quantiles[i].size() == 0) {
//in case this is not a distance found in your template files
for (int g = 0; g < 6; g++) {
- quantiles[i].push_back(0.0);
+ temp.push_back(0.0);
}
}else{
sort(quantiles[i].begin(), quantiles[i].end());
- vector<float> temp;
//save 10%
temp.push_back(quantiles[i][int(quantiles[i].size() * 0.10)]);
//save 25%
//save 99%
temp.push_back(quantiles[i][int(quantiles[i].size() * 0.99)]);
- quantiles[i] = temp;
}
//output quan value
out4 << i+1 << '\t';
- for (int u = 0; u < quantiles[i].size(); u++) { out4 << quantiles[i][u] << '\t'; }
+ for (int u = 0; u < temp.size(); u++) { out4 << temp[u] << '\t'; }
out4 << endl;
-
+
+ quantiles[i] = temp;
+
}
+ out4.close();
+
mothurOut("Done."); mothurOutEndLine();
+
}
-
+
//free memory
for (int i = 0; i < lines.size(); i++) { delete lines[i]; }
for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i]; }
}
}
- seqsMatches.push_back(match);
+ //make copy so trimSeqs doesn't overtrim
+ Sequence* copy = new Sequence(match->getName(), match->getAligned());
+
+ seqsMatches.push_back(copy);
}
return seqsMatches;
//chops off beginning and end of sequences so they both start and end with a base
map<int, int> trim;
+
decalc->trimSeqs(querySeqs[j], bestfit[j], trim);
trimmed[j] = trim;
//output trimmed values
for (int i = lines[process]->start; i < lines[process]->end; i++) {
- it = trimmed[i].begin();
-
+ it = trimmed[i].begin();
out << it->first << '\t' << it->second << endl;
}
out.close();
for (int m = 0; m < size; m++) {
int front, back;
in >> front >> back;
-
+
map<int, int> t;
t[front] = back;
for (int i = lines[0]->start; i < lines[0]->end; i++) {
it = trimmed[i].begin();
- map<int, int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
- windows[i] = win;
+ vector<int> win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment);
+ windowsForeachQuery[i] = win;
}
#endif
#else
mothurOut("Calculating observed distance... "); cout.flush();
for (int i = lines[0]->start; i < lines[0]->end; i++) {
- vector<float> obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windows[i], windowSizes[i]);
+ vector<float> obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]);
obsDistance[i] = obsi;
}
mothurOut("Done."); mothurOutEndLine();
mothurOut("Finding variability... "); cout.flush();
for (int i = lines[0]->start; i < lines[0]->end; i++) {
- vector<float> q = decalc->findQav(windows[i], windowSizes[i], probabilityProfile, h[i]);
+ vector<float> q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile);
Qav[i] = q;
}
mothurOut("Done."); mothurOutEndLine();
process++;
}else if (pid == 0){
- quantiles = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
+ quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end, makeCompliant);
//write out data to file so parent can read it
ofstream out;
//output observed distances
- for (int i = 0; i < quantiles.size(); i++) {
- out << quantiles[i].size() << '\t';
- for (int j = 0; j < quantiles[i].size(); j++) {
- out << quantiles[i][j] << '\t';
+ for (int i = 0; i < quantilesMembers.size(); i++) {
+ out << quantilesMembers[i].size() << '\t';
+ for (int j = 0; j < quantilesMembers[i].size(); j++) {
+ out << quantilesMembers[i][j].score << '\t' << quantilesMembers[i][j].member1 << '\t' << quantilesMembers[i][j].member2 << '\t';
}
out << endl;
}
int temp = processIDS[i];
wait(&temp);
}
-
+
//get data created by processes
for (int i=0;i<processors;i++) {
ifstream in;
string s = toString(processIDS[i]) + ".temp";
openInputFile(s, in);
- vector< vector<float> > quan; quan.resize(100);
+ vector< vector<quanMember> > quan;
+ quan.resize(100);
//get quantiles
for (int m = 0; m < quan.size(); m++) {
int num;
- in >> num;
-
- vector<float> q; float w;
+ in >> num;
+
+ gobble(in);
+
+ vector<quanMember> q; float w; int b, n;
for (int j = 0; j < num; j++) {
- in >> w;
- q.push_back(w);
+ in >> w >> b >> n;
+ //cout << w << '\t' << b << '\t' n << endl;
+ quanMember newMember(w, b, n);
+ q.push_back(newMember);
}
-
+//cout << "here" << endl;
quan[m] = q;
+//cout << "now here" << endl;
gobble(in);
}
-
+
//save quan in quantiles
- for (int i = 0; i < quan.size(); i++) {
+ for (int j = 0; j < quan.size(); j++) {
//put all values of q[i] into quan[i]
- quantiles[i].insert(quantiles[i].begin(), quan[i].begin(), quan[i].end());
+ for (int l = 0; l < quan[j].size(); l++) { quantilesMembers[j].push_back(quan[j][l]); }
+ //quantilesMembers[j].insert(quantilesMembers[j].begin(), quan[j].begin(), quan[j].end());
}
in.close();
}
#else
- quantiles = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
+ quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size(), makeCompliant);
#endif
}
catch(exception& e) {
projects / mothur.git / blobdiff