#include "bayesian.h"
#include "kmer.hpp"
#include "phylosummary.h"
-
+#include "referencedb.h"
/**************************************************************************************************/
-Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i) :
+Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i, int tid) :
Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
try {
+ ReferenceDB* rdb = ReferenceDB::getInstance();
+
+ threadID = tid;
+ string baseName = tempFile;
+
+ if (baseName == "saved") { baseName = rdb->getSavedReference(); }
+
+ string baseTName = tfile;
+ if (baseTName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
/************calculate the probablity that each word will be in a specific taxonomy*************/
- string tfileroot = tfile.substr(0,tfile.find_last_of(".")+1);
- string tempfileroot = m->getRootName(m->getSimpleName(tempFile));
+ string tfileroot = baseTName.substr(0,baseTName.find_last_of(".")+1);
+ string tempfileroot = m->getRootName(m->getSimpleName(baseName));
string phyloTreeName = tfileroot + "tree.train";
string phyloTreeSumName = tfileroot + "tree.sum";
string probFileName = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.prob";
FilesGood = checkReleaseDate(probFileTest, probFileTest2, phyloTreeTest, probFileTest3);
}
+ //if you want to save, but you dont need to calculate then just read
+ if (rdb->save && probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood && (tempFile != "saved")) {
+ ifstream saveIn;
+ m->openInputFile(tempFile, saveIn);
+
+ while (!saveIn.eof()) {
+ Sequence temp(saveIn);
+ m->gobble(saveIn);
+
+ rdb->referenceSeqs.push_back(temp);
+ }
+ saveIn.close();
+ }
+
if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood){
+ if (tempFile == "saved") { m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine(); }
+
m->mothurOut("Reading template taxonomy... "); cout.flush();
phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
genusNodes = phyloTree->getGenusNodes();
genusTotals = phyloTree->getGenusTotals();
-
- m->mothurOut("Reading template probabilities... "); cout.flush();
- readProbFile(probFileTest, probFileTest2, probFileName, probFileName2);
+ if (tfile == "saved") {
+ m->mothurOutEndLine(); m->mothurOut("Using probabilties from " + rdb->getSavedTaxonomy() + " that are saved in memory... "); cout.flush();;
+ wordGenusProb = rdb->wordGenusProb;
+ }else {
+ m->mothurOut("Reading template probabilities... "); cout.flush();
+ readProbFile(probFileTest, probFileTest2, probFileName, probFileName2);
+ }
+
+ //save probabilities
+ if (rdb->save) { rdb->wordGenusProb = wordGenusProb; }
}else{
//create search database and names vector
generateDatabaseAndNames(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0);
//prevents errors caused by creating shortcut files if you had an error in the sanity check.
- if (m->control_pressed) { remove(phyloTreeName.c_str()); remove(probFileName.c_str()); remove(probFileName2.c_str()); }
+ if (m->control_pressed) { m->mothurRemove(phyloTreeName); m->mothurRemove(probFileName); m->mothurRemove(probFileName2); }
else{
genusNodes = phyloTree->getGenusNodes();
genusTotals = phyloTree->getGenusTotals();
//cout << numKmers << '\t' << genusNodes.size() << endl;
for (int j = 0; j < wordGenusProb.size(); j++) { wordGenusProb[j].resize(genusNodes.size()); }
//cout << numKmers << '\t' << genusNodes.size() << endl;
- ofstream out;
- ofstream out2;
+ //ofstream out;
+ //ofstream out2;
#ifdef USE_MPI
int pid;
#endif
- m->openOutputFile(probFileName, out);
+ //m->openOutputFile(probFileName, out);
//output mothur version
- out << "#" << m->getVersion() << endl;
+ //out << "#" << m->getVersion() << endl;
- out << numKmers << endl;
+ //out << numKmers << endl;
- m->openOutputFile(probFileName2, out2);
+ //m->openOutputFile(probFileName2, out2);
//output mothur version
- out2 << "#" << m->getVersion() << endl;
+ //out2 << "#" << m->getVersion() << endl;
#ifdef USE_MPI
}
if (pid == 0) {
#endif
- out << i << '\t';
+ //out << i << '\t';
#ifdef USE_MPI
}
if (pid == 0) {
#endif
- out << k << '\t' << wordGenusProb[i][k] << '\t';
+ //out << k << '\t' << wordGenusProb[i][k] << '\t';
#ifdef USE_MPI
}
if (pid == 0) {
#endif
- out << endl;
- out2 << probabilityInTemplate << '\t' << numNotZero << endl;
+ //out << endl;
+ //out2 << probabilityInTemplate << '\t' << numNotZero << endl;
#ifdef USE_MPI
}
if (pid == 0) {
#endif
- out.close();
- out2.close();
+ //out.close();
+ //out2.close();
#ifdef USE_MPI
}
delete phyloTree;
phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
+
+ //save probabilities
+ if (rdb->save) { rdb->wordGenusProb = wordGenusProb; }
}
}
//bootstrap - to set confidenceScore
int numToSelect = queryKmers.size() / 8;
-// tax = bootstrapResults(queryKmers, index, numToSelect);
+ tax = bootstrapResults(queryKmers, index, numToSelect);
return tax;
}
//find taxonomy with highest probability that this sequence is from it
- cout << genusNodes.size() << endl;
+// cout << genusNodes.size() << endl;
for (int k = 0; k < genusNodes.size(); k++) {
prob += wordGenusProb[queryKmer[i]][k];
}
- cout << phyloTree->get(genusNodes[k]).name << '\t' << prob << endl;
+// cout << phyloTree->get(genusNodes[k]).name << '\t' << prob << endl;
//is this the taxonomy with the greatest probability?
if (prob > maxProbability) {
#ifdef USE_MPI
int pid, num, num2, processors;
- vector<unsigned long int> positions;
- vector<unsigned long int> positions2;
+ vector<unsigned long long> positions;
+ vector<unsigned long long> positions2;
MPI_Status status;
MPI_File inMPI;
string line = m->getline(in); m->gobble(in);
in >> numKmers; m->gobble(in);
-
+ //cout << threadID << '\t' << line << '\t' << numKmers << &in << '\t' << &inNum << '\t' << genusNodes.size() << endl;
//initialze probabilities
wordGenusProb.resize(numKmers);
//read version
string line2 = m->getline(inNum); m->gobble(inNum);
-
+ //cout << threadID << '\t' << line2 << '\t' << this << endl;
while (inNum) {
inNum >> zeroCountProb[count] >> num[count];
count++;
m->gobble(inNum);
+ //cout << threadID << '\t' << count << endl;
}
inNum.close();
-
+ //cout << threadID << '\t' << "here1 " << &wordGenusProb << '\t' << &num << endl; //
+ //cout << threadID << '\t' << &genusTotals << '\t' << endl;
+ //cout << threadID << '\t' << genusNodes.size() << endl;
while(in) {
in >> kmer;
-
+ //cout << threadID << '\t' << kmer << endl;
//set them all to zero value
for (int i = 0; i < genusNodes.size(); i++) {
wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
}
-
+ //cout << threadID << '\t' << num[kmer] << "here" << endl;
//get probs for nonzero values
for (int i = 0; i < num[kmer]; i++) {
in >> name >> prob;
m->gobble(in);
}
in.close();
-
+ //cout << threadID << '\t' << "here" << endl;
#endif
}
catch(exception& e) {