#include "suffixdb.hpp"
#include "blastdb.hpp"
#include "distancedb.hpp"
+#include "referencedb.h"
/**************************************************************************************************/
void Classify::generateDatabaseAndNames(string tfile, string tempFile, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch) {
try {
- taxFile = tfile;
- readTaxonomy(taxFile);
+ ReferenceDB* rdb = ReferenceDB::getInstance();
- templateFile = tempFile;
+ if (tfile == "saved") { tfile = rdb->getSavedTaxonomy(); }
- int start = time(NULL);
- int numSeqs = 0;
+ taxFile = tfile;
- m->mothurOut("Generating search database... "); cout.flush();
-#ifdef USE_MPI
- int pid, processors;
- vector<unsigned long int> positions;
- int tag = 2001;
+ int numSeqs = 0;
- MPI_Status status;
- MPI_File inMPI;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
- //char* inFileName = new char[tempFile.length()];
- //memcpy(inFileName, tempFile.c_str(), tempFile.length());
+ if (tempFile == "saved") {
+ int start = time(NULL);
+ m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine();
- char inFileName[1024];
- strcpy(inFileName, tempFile.c_str());
-
- MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
- //delete inFileName;
-
- if (pid == 0) { //only one process needs to scan file
- positions = m->setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs
-
- //send file positions to all processes
- for(int i = 1; i < processors; i++) {
- MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ numSeqs = rdb->referenceSeqs.size();
+ templateFile = rdb->getSavedReference();
+ tempFile = rdb->getSavedReference();
+
+ bool needToGenerate = true;
+ string kmerDBName;
+ if(method == "kmer") {
+ database = new KmerDB(tempFile, kmerSize);
+
+ kmerDBName = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+ ifstream kmerFileTest(kmerDBName.c_str());
+ if(kmerFileTest){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
+ if (GoodFile) { needToGenerate = false; }
}
- }else{
- MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- positions.resize(numSeqs+1);
- MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
}
-
- //create database
- if(method == "kmer") { database = new KmerDB(tempFile, kmerSize); }
else if(method == "suffix") { database = new SuffixDB(numSeqs); }
- else if(method == "blast") { database = new BlastDB(gapOpen, gapExtend, match, misMatch); }
+ else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID); }
else if(method == "distance") { database = new DistanceDB(); }
else {
- m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();
+ m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
+ m->mothurOutEndLine();
database = new KmerDB(tempFile, 8);
}
-
- //read file
- for(int i=0;i<numSeqs;i++){
- //read next sequence
- int length = positions[i+1] - positions[i];
- char* buf4 = new char[length];
- MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
-
- string tempBuf = buf4;
- if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
- delete buf4;
- istringstream iss (tempBuf,istringstream::in);
-
- Sequence temp(iss);
- if (temp.getName() != "") {
+
+ if (needToGenerate) {
+ for (int k = 0; k < rdb->referenceSeqs.size(); k++) {
+ Sequence temp(rdb->referenceSeqs[k].getName(), rdb->referenceSeqs[k].getAligned());
names.push_back(temp.getName());
database->addSequence(temp);
}
- }
+ if ((method == "kmer") && (!shortcuts)) {;} //don't print
+ else {database->generateDB(); }
+ }else if ((method == "kmer") && (!needToGenerate)) {
+ ifstream kmerFileTest(kmerDBName.c_str());
+ database->readKmerDB(kmerFileTest);
+
+ for (int k = 0; k < rdb->referenceSeqs.size(); k++) {
+ names.push_back(rdb->referenceSeqs[k].getName());
+ }
+ }
- database->generateDB();
- MPI_File_close(&inMPI);
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- #else
-
- //need to know number of template seqs for suffixdb
- if (method == "suffix") {
- ifstream inFASTA;
- m->openInputFile(tempFile, inFASTA);
- m->getNumSeqs(inFASTA, numSeqs);
- inFASTA.close();
- }
-
- bool needToGenerate = true;
- string kmerDBName;
- if(method == "kmer") {
- database = new KmerDB(tempFile, kmerSize);
+ database->setNumSeqs(numSeqs);
- kmerDBName = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
- ifstream kmerFileTest(kmerDBName.c_str());
- if(kmerFileTest){
- bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
- if (GoodFile) { needToGenerate = false; }
- }
- }
- else if(method == "suffix") { database = new SuffixDB(numSeqs); }
- else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch); }
- else if(method == "distance") { database = new DistanceDB(); }
- else {
- m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
- m->mothurOutEndLine();
- database = new KmerDB(tempFile, 8);
- }
-
- if (needToGenerate) {
- ifstream fastaFile;
- m->openInputFile(tempFile, fastaFile);
+ m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences and generate the search databases.");m->mothurOutEndLine();
- while (!fastaFile.eof()) {
- Sequence temp(fastaFile);
- m->gobble(fastaFile);
+ }else {
- names.push_back(temp.getName());
-
- database->addSequence(temp);
- }
- fastaFile.close();
+ templateFile = tempFile;
+
+ int start = time(NULL);
+
+ m->mothurOut("Generating search database... "); cout.flush();
+ #ifdef USE_MPI
+ int pid, processors;
+ vector<unsigned long long> positions;
+ int tag = 2001;
+
+ MPI_Status status;
+ MPI_File inMPI;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ //char* inFileName = new char[tempFile.length()];
+ //memcpy(inFileName, tempFile.c_str(), tempFile.length());
+
+ char inFileName[1024];
+ strcpy(inFileName, tempFile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ //delete inFileName;
- database->generateDB();
+ if (pid == 0) { //only one process needs to scan file
+ positions = m->setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+ }else{
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ positions.resize(numSeqs+1);
+ MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+ }
+
+ //create database
+ if(method == "kmer") { database = new KmerDB(tempFile, kmerSize); }
+ else if(method == "suffix") { database = new SuffixDB(numSeqs); }
+ else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", pid); }
+ else if(method == "distance") { database = new DistanceDB(); }
+ else {
+ m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();
+ database = new KmerDB(tempFile, 8);
+ }
+
+ //read file
+ for(int i=0;i<numSeqs;i++){
+ //read next sequence
+ int length = positions[i+1] - positions[i];
+ char* buf4 = new char[length];
+ MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ delete buf4;
+ istringstream iss (tempBuf,istringstream::in);
+
+ Sequence temp(iss);
+ if (temp.getName() != "") {
+ if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
+ names.push_back(temp.getName());
+ database->addSequence(temp);
+ }
+ }
+
+ database->generateDB();
+ MPI_File_close(&inMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+ #else
- }else if ((method == "kmer") && (!needToGenerate)) {
- ifstream kmerFileTest(kmerDBName.c_str());
- database->readKmerDB(kmerFileTest);
-
- ifstream fastaFile;
- m->openInputFile(tempFile, fastaFile);
+ //need to know number of template seqs for suffixdb
+ if (method == "suffix") {
+ ifstream inFASTA;
+ m->openInputFile(tempFile, inFASTA);
+ m->getNumSeqs(inFASTA, numSeqs);
+ inFASTA.close();
+ }
+
+ bool needToGenerate = true;
+ string kmerDBName;
+ if(method == "kmer") {
+ database = new KmerDB(tempFile, kmerSize);
+
+ kmerDBName = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+ ifstream kmerFileTest(kmerDBName.c_str());
+ if(kmerFileTest){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
+ if (GoodFile) { needToGenerate = false; }
+ }
+ }
+ else if(method == "suffix") { database = new SuffixDB(numSeqs); }
+ else if(method == "blast") { database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID); }
+ else if(method == "distance") { database = new DistanceDB(); }
+ else {
+ m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
+ m->mothurOutEndLine();
+ database = new KmerDB(tempFile, 8);
+ }
- while (!fastaFile.eof()) {
- Sequence temp(fastaFile);
- m->gobble(fastaFile);
+ if (needToGenerate) {
+ ifstream fastaFile;
+ m->openInputFile(tempFile, fastaFile);
+
+ while (!fastaFile.eof()) {
+ Sequence temp(fastaFile);
+ m->gobble(fastaFile);
+
+ if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
+
+ names.push_back(temp.getName());
+
+ database->addSequence(temp);
+ }
+ fastaFile.close();
- names.push_back(temp.getName());
+ if ((method == "kmer") && (!shortcuts)) {;} //don't print
+ else {database->generateDB(); }
+
+ }else if ((method == "kmer") && (!needToGenerate)) {
+ ifstream kmerFileTest(kmerDBName.c_str());
+ database->readKmerDB(kmerFileTest);
+
+ ifstream fastaFile;
+ m->openInputFile(tempFile, fastaFile);
+
+ while (!fastaFile.eof()) {
+ Sequence temp(fastaFile);
+ m->gobble(fastaFile);
+
+ if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
+ names.push_back(temp.getName());
+ }
+ fastaFile.close();
}
- fastaFile.close();
+ #endif
+
+ database->setNumSeqs(names.size());
+
+ m->mothurOut("DONE."); m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
}
-#endif
-
- database->setNumSeqs(names.size());
-
- //sanity check
- bool okay = phyloTree->ErrorCheck(names);
-
- if (!okay) { m->control_pressed = true; }
-
- m->mothurOut("DONE."); m->mothurOutEndLine();
- m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
-
+
+ readTaxonomy(taxFile);
+
+ //sanity check
+ bool okay = phyloTree->ErrorCheck(names);
+
+ if (!okay) { m->control_pressed = true; }
}
catch(exception& e) {
m->errorOut(e, "Classify", "generateDatabaseAndNames");
}
}
/**************************************************************************************************/
-Classify::Classify() { m = MothurOut::getInstance(); database = NULL; }
+Classify::Classify() { m = MothurOut::getInstance(); database = NULL; phyloTree=NULL; flipped=false; }
/**************************************************************************************************/
int Classify::readTaxonomy(string file) {
m->mothurOutEndLine();
m->mothurOut("Reading in the " + file + " taxonomy...\t"); cout.flush();
-
+ if (m->debug) { m->mothurOut("[DEBUG]: Taxonomies read in...\n"); }
+
#ifdef USE_MPI
int pid, num, processors;
- vector<unsigned long int> positions;
+ vector<unsigned long long> positions;
int tag = 2001;
MPI_Status status;
MPI_File inMPI;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
- //char* inFileName = new char[file.length()];
- //memcpy(inFileName, file.c_str(), file.length());
char inFileName[1024];
strcpy(inFileName, file.c_str());
delete buf4;
istringstream iss (tempBuf,istringstream::in);
- iss >> name >> taxInfo;
- taxonomy[name] = taxInfo;
- phyloTree->addSeqToTree(name, taxInfo);
- }
+ iss >> name; m->gobble(iss);
+ iss >> taxInfo;
+ if (m->debug) { m->mothurOut("[DEBUG]: name = " + name + " tax = " + taxInfo + "\n"); }
+ if (m->inUsersGroups(name, names)) {
+ taxonomy[name] = taxInfo;
+ phyloTree->addSeqToTree(name, taxInfo);
+ }else {
+ m->mothurOut("[WARNING]: " + name + " is in your taxonomy file and not in your reference file, ignoring.\n");
+ }
+ }
MPI_File_close(&inMPI);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-#else
- ifstream inTax;
- m->openInputFile(file, inTax);
-
- //read template seqs and save
- while (!inTax.eof()) {
- inTax >> name >> taxInfo;
-
- taxonomy[name] = taxInfo;
-
- phyloTree->addSeqToTree(name, taxInfo);
-
- m->gobble(inTax);
- }
- inTax.close();
+#else
+
+ taxonomy.clear();
+ m->readTax(file, taxonomy);
+ map<string, string> tempTaxonomy;
+ for (map<string, string>::iterator itTax = taxonomy.begin(); itTax != taxonomy.end(); itTax++) {
+ if (m->inUsersGroups(itTax->first, names)) {
+ phyloTree->addSeqToTree(itTax->first, itTax->second);
+ tempTaxonomy[itTax->first] = itTax->second;
+ }else {
+ m->mothurOut("[WARNING]: " + itTax->first + " is in your taxonomy file and not in your reference file, ignoring.\n");
+ }
+ }
+ taxonomy = tempTaxonomy;
#endif
-
phyloTree->assignHeirarchyIDs(0);
phyloTree->setUp(file);
}
/**************************************************************************************************/
+double Classify::getLogExpSum(vector<double> probabilities, int& maxIndex){
+ try {
+ // http://jblevins.org/notes/log-sum-exp
+
+ double maxProb = probabilities[0];
+ maxIndex = 0;
+
+ int numProbs = (int)probabilities.size();
+
+ for(int i=1;i<numProbs;i++){
+ if(probabilities[i] >= maxProb){
+ maxProb = probabilities[i];
+ maxIndex = i;
+ }
+ }
+
+ double probSum = 0.0000;
+
+ for(int i=0;i<numProbs;i++){
+ probSum += exp(probabilities[i] - maxProb);
+ }
+
+ probSum = log(probSum) + maxProb;
+
+ return probSum;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Classify", "getLogExpSum");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
projects / mothur.git / blobdiff