/************calculate the probablity that each word will be in a specific taxonomy*************/
string tfileroot = tfile.substr(0,tfile.find_last_of(".")+1);
- string tempfileroot = getRootName(getSimpleName(tempFile));
+ string tempfileroot = m->getRootName(m->getSimpleName(tempFile));
string phyloTreeName = tfileroot + "tree.train";
string phyloTreeSumName = tfileroot + "tree.sum";
string probFileName = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.prob";
int start = time(NULL);
- if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3){
+ //if they are there make sure they were created after this release date
+ bool FilesGood = false;
+ if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3){
+ FilesGood = checkReleaseDate(probFileTest, probFileTest2, phyloTreeTest, probFileTest3);
+ }
+
+ if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood){
m->mothurOut("Reading template taxonomy... "); cout.flush();
phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
//initialze probabilities
wordGenusProb.resize(numKmers);
-
+ //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;
#endif
- openOutputFile(probFileName, out);
+ m->openOutputFile(probFileName, out);
+
+ //output mothur version
+ out << "#" << m->getVersion() << endl;
out << numKmers << endl;
- openOutputFile(probFileName2, out2);
+ m->openOutputFile(probFileName2, out2);
+
+ //output mothur version
+ out2 << "#" << m->getVersion() << endl;
#ifdef USE_MPI
}
MPI_File_open(MPI_COMM_WORLD, inFileName2, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI2); //comm, filename, mode, info, filepointer
if (pid == 0) {
- positions = setFilePosEachLine(inNumName, num);
- positions2 = setFilePosEachLine(inName, num2);
+ positions = m->setFilePosEachLine(inNumName, num);
+ positions2 = m->setFilePosEachLine(inName, num2);
for(int i = 1; i < processors; i++) {
MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
positions2.resize(num2+1);
MPI_Recv(&positions2[0], (num2+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
}
-
- //read numKmers
+
+ //read version
int length = positions2[1] - positions2[0];
+ char* buf5 = new char[length];
+
+ MPI_File_read_at(inMPI2, positions2[0], buf5, length, MPI_CHAR, &status);
+ delete buf5;
+
+ //read numKmers
+ length = positions2[2] - positions2[1];
char* buf = new char[length];
- MPI_File_read_at(inMPI2, positions2[0], buf, length, MPI_CHAR, &status);
+ MPI_File_read_at(inMPI2, positions2[1], buf, length, MPI_CHAR, &status);
string tempBuf = buf;
if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
int kmer, name;
vector<int> numbers; numbers.resize(numKmers);
float prob;
- vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
+ vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
+
+ //read version
+ length = positions[1] - positions[0];
+ char* buf6 = new char[length];
+ MPI_File_read_at(inMPI2, positions[0], buf6, length, MPI_CHAR, &status);
+ delete buf6;
+
//read file
- for(int i=0;i<num;i++){
+ for(int i=1;i<num;i++){
//read next sequence
length = positions[i+1] - positions[i];
char* buf4 = new char[length];
MPI_File_close(&inMPI);
- for(int i=1;i<num2;i++){
+ for(int i=2;i<num2;i++){
//read next sequence
length = positions2[i+1] - positions2[i];
char* buf4 = new char[length];
MPI_File_close(&inMPI2);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
-
- in >> numKmers; gobble(in);
+ //read version
+ string line = m->getline(in); m->gobble(in);
+
+ in >> numKmers; m->gobble(in);
//initialze probabilities
wordGenusProb.resize(numKmers);
vector<int> num; num.resize(numKmers);
float prob;
vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
-
+
+ //read version
+ string line2 = m->getline(inNum); m->gobble(inNum);
+
while (inNum) {
inNum >> zeroCountProb[count] >> num[count];
count++;
- gobble(inNum);
+ m->gobble(inNum);
}
inNum.close();
wordGenusProb[kmer][name] = prob;
}
- gobble(in);
+ m->gobble(in);
}
in.close();
}
}
/**************************************************************************************************/
+bool Bayesian::checkReleaseDate(ifstream& file1, ifstream& file2, ifstream& file3, ifstream& file4) {
+ try {
+
+ bool good = true;
+
+ vector<string> lines;
+ lines.push_back(m->getline(file1));
+ lines.push_back(m->getline(file2));
+ lines.push_back(m->getline(file3));
+ lines.push_back(m->getline(file4));
+
+ //before we added this check
+ if ((lines[0][0] != '#') || (lines[1][0] != '#') || (lines[2][0] != '#') || (lines[3][0] != '#')) { good = false; }
+ else {
+ //rip off #
+ for (int i = 0; i < lines.size(); i++) { lines[i] = lines[i].substr(1); }
+
+ //get mothurs current version
+ string version = m->getVersion();
+
+ vector<string> versionVector;
+ m->splitAtChar(version, versionVector, '.');
+
+ //check each files version
+ for (int i = 0; i < lines.size(); i++) {
+ vector<string> linesVector;
+ m->splitAtChar(lines[i], linesVector, '.');
+
+ if (versionVector.size() != linesVector.size()) { good = false; break; }
+ else {
+ for (int j = 0; j < versionVector.size(); j++) {
+ int num1, num2;
+ convert(versionVector[j], num1);
+ convert(linesVector[j], num2);
+
+ //if mothurs version is newer than this files version, then we want to remake it
+ if (num1 > num2) { good = false; break; }
+ }
+ }
+
+ if (!good) { break; }
+ }
+ }
+
+ if (!good) { file1.close(); file2.close(); file3.close(); file4.close(); }
+ else { file1.seekg(0); file2.seekg(0); file3.seekg(0); file4.seekg(0); }
+
+ return good;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Bayesian", "checkReleaseDate");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
projects / mothur.git / blobdiff