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()); }
-
- genusNodes = phyloTree->getGenusNodes();
- genusTotals = phyloTree->getGenusTotals();
-
- m->mothurOut("Calculating template taxonomy tree... "); cout.flush();
-
- phyloTree->printTreeNodes(phyloTreeName);
-
- m->mothurOut("DONE."); m->mothurOutEndLine();
-
- m->mothurOut("Calculating template probabilities... "); cout.flush();
-
- numKmers = database->getMaxKmer() + 1;
-
- //initialze probabilities
- wordGenusProb.resize(numKmers);
-
- for (int j = 0; j < wordGenusProb.size(); j++) { wordGenusProb[j].resize(genusNodes.size()); }
-
-
- #ifdef USE_MPI
- int pid;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
-
- ofstream out;
- openOutputFile(probFileName, out);
-
- out << numKmers << endl;
-
- ofstream out2;
- openOutputFile(probFileName2, out2);
+ if (m->control_pressed) { remove(phyloTreeName.c_str()); remove(probFileName.c_str()); remove(probFileName2.c_str()); }
+ else{
+ genusNodes = phyloTree->getGenusNodes();
+ genusTotals = phyloTree->getGenusTotals();
+
+ m->mothurOut("Calculating template taxonomy tree... "); cout.flush();
+
+ phyloTree->printTreeNodes(phyloTreeName);
+
+ m->mothurOut("DONE."); m->mothurOutEndLine();
+
+ m->mothurOut("Calculating template probabilities... "); cout.flush();
+
+ numKmers = database->getMaxKmer() + 1;
- #ifdef USE_MPI
- }
- #endif
-
+ //initialze probabilities
+ wordGenusProb.resize(numKmers);
- //for each word
- for (int i = 0; i < numKmers; i++) {
- if (m->control_pressed) { break; }
+ for (int j = 0; j < wordGenusProb.size(); j++) { wordGenusProb[j].resize(genusNodes.size()); }
+
#ifdef USE_MPI
+ int pid;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
if (pid == 0) {
#endif
- out << i << '\t';
+ ofstream out;
+ openOutputFile(probFileName, out);
+
+ out << numKmers << endl;
+
+ ofstream out2;
+ openOutputFile(probFileName2, out2);
#ifdef USE_MPI
}
#endif
+
- vector<int> seqsWithWordi = database->getSequencesWithKmer(i);
-
- map<int, int> count;
- for (int k = 0; k < genusNodes.size(); k++) { count[genusNodes[k]] = 0; }
-
- //for each sequence with that word
- for (int j = 0; j < seqsWithWordi.size(); j++) {
- int temp = phyloTree->getIndex(names[seqsWithWordi[j]]);
- count[temp]++; //increment count of seq in this genus who have this word
- }
-
- //probabilityInTemplate = (# of seqs with that word in template + 0.05) / (total number of seqs in template + 1);
- float probabilityInTemplate = (seqsWithWordi.size() + 0.50) / (float) (names.size() + 1);
-
- int numNotZero = 0;
- for (int k = 0; k < genusNodes.size(); k++) {
- //probabilityInThisTaxonomy = (# of seqs with that word in this taxonomy + probabilityInTemplate) / (total number of seqs in this taxonomy + 1);
- wordGenusProb[i][k] = log((count[genusNodes[k]] + probabilityInTemplate) / (float) (genusTotals[k] + 1));
- if (count[genusNodes[k]] != 0) {
- #ifdef USE_MPI
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- if (pid == 0) {
- #endif
+ //for each word
+ for (int i = 0; i < numKmers; i++) {
+ if (m->control_pressed) { break; }
+
+ #ifdef USE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- out << k << '\t' << wordGenusProb[i][k] << '\t';
-
- #ifdef USE_MPI
- }
- #endif
+ if (pid == 0) {
+ #endif
- numNotZero++;
+ out << i << '\t';
+
+ #ifdef USE_MPI
+ }
+ #endif
+
+ vector<int> seqsWithWordi = database->getSequencesWithKmer(i);
+
+ map<int, int> count;
+ for (int k = 0; k < genusNodes.size(); k++) { count[genusNodes[k]] = 0; }
+
+ //for each sequence with that word
+ for (int j = 0; j < seqsWithWordi.size(); j++) {
+ int temp = phyloTree->getIndex(names[seqsWithWordi[j]]);
+ count[temp]++; //increment count of seq in this genus who have this word
}
+
+ //probabilityInTemplate = (# of seqs with that word in template + 0.05) / (total number of seqs in template + 1);
+ float probabilityInTemplate = (seqsWithWordi.size() + 0.50) / (float) (names.size() + 1);
+
+ int numNotZero = 0;
+ for (int k = 0; k < genusNodes.size(); k++) {
+ //probabilityInThisTaxonomy = (# of seqs with that word in this taxonomy + probabilityInTemplate) / (total number of seqs in this taxonomy + 1);
+ wordGenusProb[i][k] = log((count[genusNodes[k]] + probabilityInTemplate) / (float) (genusTotals[k] + 1));
+ if (count[genusNodes[k]] != 0) {
+ #ifdef USE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ if (pid == 0) {
+ #endif
+
+ out << k << '\t' << wordGenusProb[i][k] << '\t';
+
+ #ifdef USE_MPI
+ }
+ #endif
+
+ numNotZero++;
+ }
+ }
+
+ #ifdef USE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ if (pid == 0) {
+ #endif
+
+ out << endl;
+ out2 << probabilityInTemplate << '\t' << numNotZero << endl;
+
+ #ifdef USE_MPI
+ }
+ #endif
}
#ifdef USE_MPI
if (pid == 0) {
#endif
- out << endl;
- out2 << probabilityInTemplate << '\t' << numNotZero << endl;
+ out.close();
+ out2.close();
#ifdef USE_MPI
}
#endif
+
+ //read in new phylotree with less info. - its faster
+ ifstream phyloTreeTest(phyloTreeName.c_str());
+ delete phyloTree;
+
+ phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
}
-
- #ifdef USE_MPI
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- if (pid == 0) {
- #endif
-
- out.close();
- out2.close();
-
- #ifdef USE_MPI
- }
- #endif
-
- //read in new phylotree with less info. - its faster
- ifstream phyloTreeTest(phyloTreeName.c_str());
- delete phyloTree;
-
- phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
}
m->mothurOut("DONE."); m->mothurOutEndLine();
projects / mothur.git / blobdiff