}
//***************************************************************************************************************
-Pintail::Pintail(string filename, string o) {
- fastafile = filename; outputDir = o;
- distcalculator = new eachGapDist();
- decalc = new DeCalculator();
+Pintail::Pintail(string filename, string temp, bool f, int p, string mask, string cons, string q, int win, int inc, string o) : Chimera() {
+ try {
+
+ fastafile = filename;
+ templateFileName = temp; templateSeqs = readSeqs(temp);
+ filter = f;
+ processors = p;
+ setMask(mask);
+ consfile = cons;
+ quanfile = q;
+ window = win;
+ increment = inc;
+ outputDir = o;
+
+ distcalculator = new eachGapDist();
+ decalc = new DeCalculator();
+
+ doPrep();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Pintail", "Pintail");
+ exit(1);
+ }
+
}
//***************************************************************************************************************
delete decalc;
}
catch(exception& e) {
- errorOut(e, "Pintail", "~Pintail");
+ m->errorOut(e, "Pintail", "~Pintail");
exit(1);
}
}
//***************************************************************************************************************
-void Pintail::doPrep() {
+int Pintail::doPrep() {
try {
mergedFilterString = "";
decalc->setMask(seqMask);
+ #ifdef USE_MPI
+ //do nothing
+ #else
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//find breakup of templatefile for quantiles
if (processors == 1) { templateLines.push_back(new linePair(0, templateSeqs.size())); }
#else
templateLines.push_back(new linePair(0, templateSeqs.size()));
#endif
-
+ #endif
- mothurOut("Getting conservation... "); cout.flush();
+ m->mothurOut("Getting conservation... "); cout.flush();
if (consfile == "") {
- mothurOut("Calculating probability of conservation for your template sequences. This can take a while... I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command. Providing the .freq file will improve speed. "); cout.flush();
+ m->mothurOut("Calculating probability of conservation for your template sequences. This can take a while... I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command. Providing the .freq file will improve speed. "); cout.flush();
probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFileName));
- mothurOut("Done."); mothurOutEndLine();
- }else { probabilityProfile = readFreq(); mothurOut("Done."); }
- mothurOutEndLine();
+ if (m->control_pressed) { return 0; }
+ m->mothurOut("Done."); m->mothurOutEndLine();
+ }else { probabilityProfile = readFreq(); m->mothurOut("Done."); }
+ m->mothurOutEndLine();
//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]; } //
bool reRead = false;
//create filter if needed for later
if (filter) {
//read in all query seqs
- ifstream in;
- openInputFile(fastafile, in);
-
- vector<Sequence*> tempQuerySeqs;
- while(!in.eof()){
- Sequence* s = new Sequence(in);
- gobble(in);
+ vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
- if (s->getName() != "") { tempQuerySeqs.push_back(s); }
- }
- in.close();
-
vector<Sequence*> temp;
//merge query seqs and template seqs
temp = templateSeqs;
reRead = true;
//mask templates
for (int i = 0; i < temp.size(); i++) {
+ if (m->control_pressed) {
+ for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; }
+ return 0;
+ }
decalc->runMask(temp[i]);
}
}
mergedFilterString = createFilter(temp, 0.5);
+ if (m->control_pressed) {
+ for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; }
+ return 0;
+ }
+
//reread template seqs
for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i]; }
}
reRead = true;
//mask templates
for (int i = 0; i < templateSeqs.size(); i++) {
+ if (m->control_pressed) { return 0; }
decalc->runMask(templateSeqs[i]);
}
}
if (filter) {
reRead = true;
for (int i = 0; i < templateSeqs.size(); i++) {
+ if (m->control_pressed) { return 0; }
runFilter(templateSeqs[i]);
}
}
- 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();
+ m->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) {
quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
}else { createProcessesQuan(); }
+ if (m->control_pressed) { return 0; }
- ofstream out4, out5;
string noOutliers, outliers;
if ((!filter) && (seqMask == "")) {
noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "quan";
}
-
-
-
decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
- openOutputFile(noOutliers, out5);
+ if (m->control_pressed) { return 0; }
+
+ string outputString = "";
+
//adjust quantiles
for (int i = 0; i < quantilesMembers.size(); i++) {
vector<float> temp;
}
//output quan value
- out5 << i+1 << '\t';
- for (int u = 0; u < temp.size(); u++) { out5 << temp[u] << '\t'; }
- out5 << endl;
+ outputString += toString(i+1) + "\t";
+ for (int u = 0; u < temp.size(); u++) { outputString += toString(temp[u]) + "\t"; }
+ outputString += "\n";
quantiles[i] = temp;
}
-
- mothurOut("Done."); mothurOutEndLine();
+
+ printQuanFile(noOutliers, outputString);
+
+ m->mothurOut("Done."); m->mothurOutEndLine();
}
if (reRead) {
//free memory
for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i]; }
+ return 0;
+
}
catch(exception& e) {
- errorOut(e, "Pintail", "doPrep");
+ m->errorOut(e, "Pintail", "doPrep");
exit(1);
}
}
//***************************************************************************************************************
-void Pintail::print(ostream& out, ostream& outAcc) {
+int Pintail::print(ostream& out, ostream& outAcc) {
try {
int index = ceil(deviation);
out << querySeq->getName() << '\t' << "div: " << deviation << "\tstDev: " << DE << "\tchimera flag: " << chimera << endl;
if (chimera == "Yes") {
- mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); mothurOutEndLine();
+ m->mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); m->mothurOutEndLine();
outAcc << querySeq->getName() << endl;
}
out << "Observed\t";
for (int m = 0; m < expectedDistance.size(); m++) { out << expectedDistance[m] << '\t'; }
out << endl;
+ return 0;
}
catch(exception& e) {
- errorOut(e, "Pintail", "print");
+ m->errorOut(e, "Pintail", "print");
exit(1);
}
}
+#ifdef USE_MPI
+//***************************************************************************************************************
+int Pintail::print(MPI_File& out, MPI_File& outAcc) {
+ try {
+ bool results = false;
+ string outputString = "";
+ int index = ceil(deviation);
+
+ //is your DE value higher than the 95%
+ string chimera;
+ if (index != 0) { //if index is 0 then its an exact match to a template seq
+ if (quantiles[index][4] == 0.0) {
+ chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
+ }else {
+ if (DE > quantiles[index][4]) { chimera = "Yes"; }
+ else { chimera = "No"; }
+ }
+ }else{ chimera = "No"; }
+ outputString += querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera + "\n";
+ if (chimera == "Yes") {
+ cout << querySeq->getName() << "\tdiv: " << toString(deviation) << "\tstDev: " << toString(DE) << "\tchimera flag: " << chimera << endl;
+ string outAccString = querySeq->getName() + "\n";
+
+ MPI_Status statusAcc;
+ int length = outAccString.length();
+ char buf[length];
+ strcpy(buf, outAccString.c_str());
+
+ MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
+
+ results = true;
+ }
+ outputString += "Observed\t";
+
+ for (int j = 0; j < obsDistance.size(); j++) { outputString += toString(obsDistance[j]) + "\t"; }
+ outputString += "\n";
+
+ outputString += "Expected\t";
+
+ for (int m = 0; m < expectedDistance.size(); m++) { outputString += toString(expectedDistance[m]) + "\t"; }
+ outputString += "\n";
+
+ MPI_Status status;
+ int length = outputString.length();
+ char buf2[length];
+ strcpy(buf2, outputString.c_str());
+
+ MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
+
+ return results;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Pintail", "print");
+ exit(1);
+ }
+}
+#endif
//***************************************************************************************************************
int Pintail::getChimeras(Sequence* query) {
try {
//find pairs has to be done before a mask
bestfit = findPairs(query);
+ if (m->control_pressed) { return 0; }
+
//if they mask
if (seqMask != "") {
decalc->runMask(query);
//find observed distance
obsDistance = decalc->calcObserved(query, bestfit, windowsForeachQuery, windowSizes);
+
+ if (m->control_pressed) { return 0; }
Qav = decalc->findQav(windowsForeachQuery, windowSizes, probabilityProfile);
+
+ if (m->control_pressed) { return 0; }
//find alpha
seqCoef = decalc->getCoef(obsDistance, Qav);
//calculating expected distance
expectedDistance = decalc->calcExpected(Qav, seqCoef);
+ if (m->control_pressed) { return 0; }
+
//finding de
DE = decalc->calcDE(obsDistance, expectedDistance);
+ if (m->control_pressed) { return 0; }
+
//find distance between query and closest match
it = trimmed.begin();
deviation = decalc->calcDist(query, bestfit, it->first, it->second);
return 0;
}
catch(exception& e) {
- errorOut(e, "Pintail", "getChimeras");
+ m->errorOut(e, "Pintail", "getChimeras");
exit(1);
}
}
vector<float> Pintail::readFreq() {
try {
-
- ifstream in;
- openInputFile(consfile, in);
-
+ //read in probabilities and store in vector
+ int pos; float num;
+
vector<float> prob;
set<int> h = decalc->getPos(); //positions of bases in masking sequence
- //read in probabilities and store in vector
- int pos; float num;
+ #ifdef USE_MPI
+
+ MPI_File inMPI;
+ MPI_Offset size;
+ MPI_Status status;
+
+ char inFileName[consfile.length()];
+ strcpy(inFileName, consfile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
+ MPI_File_get_size(inMPI, &size);
+
+ char buffer[size];
+ MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
+
+ string tempBuf = buffer;
+
+ if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
+ istringstream iss (tempBuf,istringstream::in);
+
+ while(!iss.eof()) {
+ iss >> pos >> num;
+
+ if (h.count(pos) > 0) {
+ float Pi;
+ Pi = (num - 0.25) / 0.75;
+
+ //cannot have probability less than 0.
+ if (Pi < 0) { Pi = 0.0; }
+
+ //do you want this spot
+ prob.push_back(Pi);
+ }
+
+ gobble(iss);
+ }
+
+ MPI_File_close(&inMPI);
+ #else
+
+ ifstream in;
+ openInputFile(consfile, in);
+
while(!in.eof()){
in >> pos >> num;
gobble(in);
}
-
in.close();
+
+ #endif
+
return prob;
}
catch(exception& e) {
- errorOut(e, "Pintail", "readFreq");
+ m->errorOut(e, "Pintail", "readFreq");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Pintail", "findPairs");
+ m->errorOut(e, "Pintail", "findPairs");
exit(1);
}
}
-/**************************************************************************************************/
+//**************************************************************************************************
void Pintail::createProcessesQuan() {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
out.close();
exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
//force parent to wait until all the processes are done
vector<quanMember> q; float w; int b, n;
for (int j = 0; j < num; j++) {
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);
}
#endif
}
catch(exception& e) {
- errorOut(e, "Pintail", "createProcessesQuan");
+ m->errorOut(e, "Pintail", "createProcessesQuan");
exit(1);
}
}
+//***************************************************************************************************************
+vector< vector<float> > Pintail::readQuantiles() {
+ try {
+ int num;
+ float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine;
+
+ vector< vector<float> > quan;
+ vector <float> temp; temp.resize(6, 0);
+
+ //to fill 0
+ quan.push_back(temp);
+ #ifdef USE_MPI
+
+ MPI_File inMPI;
+ MPI_Offset size;
+ MPI_Status status;
+
+ char inFileName[quanfile.length()];
+ strcpy(inFileName, quanfile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
+ MPI_File_get_size(inMPI, &size);
+
+ char buffer[size];
+ MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
+
+ string tempBuf = buffer;
+ if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
+ istringstream iss (tempBuf,istringstream::in);
+
+ while(!iss.eof()) {
+ iss >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
+
+ temp.clear();
+
+ temp.push_back(ten);
+ temp.push_back(twentyfive);
+ temp.push_back(fifty);
+ temp.push_back(seventyfive);
+ temp.push_back(ninetyfive);
+ temp.push_back(ninetynine);
+
+ quan.push_back(temp);
+
+ gobble(iss);
+ }
+
+ MPI_File_close(&inMPI);
+
+ #else
+
+ ifstream in;
+ openInputFile(quanfile, in);
+
+ while(!in.eof()){
+
+ in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
+
+ temp.clear();
+
+ temp.push_back(ten);
+ temp.push_back(twentyfive);
+ temp.push_back(fifty);
+ temp.push_back(seventyfive);
+ temp.push_back(ninetyfive);
+ temp.push_back(ninetynine);
+
+ quan.push_back(temp);
+
+ gobble(in);
+ }
+ in.close();
+ #endif
+
+ return quan;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Pintail", "readQuantiles");
+ exit(1);
+ }
+}
+//***************************************************************************************************************/
+
+void Pintail::printQuanFile(string file, string outputString) {
+ try {
+
+ #ifdef USE_MPI
+
+ MPI_File outQuan;
+ MPI_Status status;
+
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ char FileName[file.length()];
+ strcpy(FileName, file.c_str());
+
+ if (pid == 0) {
+ MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outQuan); //comm, filename, mode, info, filepointer
+
+ int length = outputString.length();
+ char buf[length];
+ strcpy(buf, outputString.c_str());
+
+ MPI_File_write(outQuan, buf, length, MPI_CHAR, &status);
+
+ MPI_File_close(&outQuan);
+ }
+ #else
+ ofstream outQuan;
+ openOutputFile(file, outQuan);
+
+ outQuan << outputString;
+
+ outQuan.close();
+ #endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Pintail", "printQuanFile");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************/
-//***************************************************************************************************************
projects / mothur.git / blobdiff