+++ /dev/null
-/*
- * classify.cpp
- * Mothur
- *
- * Created by westcott on 11/3/09.
- * Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "classify.h"
-#include "sequence.hpp"
-#include "kmerdb.hpp"
-#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 {
- ReferenceDB* rdb = ReferenceDB::getInstance();
-
- if (tfile == "saved") { tfile = rdb->getSavedTaxonomy(); }
-
- taxFile = tfile;
- readTaxonomy(taxFile);
- int numSeqs = 0;
-
- if (tempFile == "saved") {
- int start = time(NULL);
- m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine();
-
- 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 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);
- }
-
- 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);
- }
- 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->setNumSeqs(numSeqs);
-
- //sanity check
- bool okay = phyloTree->ErrorCheck(names);
-
- if (!okay) { m->control_pressed = true; }
-
- m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences and generate the search databases.");m->mothurOutEndLine();
-
- }else {
-
- 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;
-
- 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
-
- //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);
- }
-
- 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();
-
- 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();
- }
- #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();
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "Classify", "generateDatabaseAndNames");
- exit(1);
- }
-}
-/**************************************************************************************************/
-Classify::Classify() { m = MothurOut::getInstance(); database = NULL; flipped=false; }
-/**************************************************************************************************/
-
-int Classify::readTaxonomy(string file) {
- try {
-
- phyloTree = new PhyloTree();
- string name, taxInfo;
-
- m->mothurOutEndLine();
- m->mothurOut("Reading in the " + file + " taxonomy...\t"); cout.flush();
-
-#ifdef USE_MPI
- int pid, num, 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[file.length()];
- //memcpy(inFileName, file.c_str(), file.length());
-
- char inFileName[1024];
- strcpy(inFileName, file.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) {
- positions = m->setFilePosEachLine(file, num);
-
- //send file positions to all processes
- for(int i = 1; i < processors; i++) {
- MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&positions[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
- }
- }else{
- MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- positions.resize(num+1);
- MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
- }
-
- //read file
- for(int i=0;i<num;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);
- iss >> name; m->gobble(iss);
- iss >> taxInfo;
- taxonomy[name] = taxInfo;
- phyloTree->addSeqToTree(name, taxInfo);
- }
-
- 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; m->gobble(inTax);
- inTax >> taxInfo;
-
- taxonomy[name] = taxInfo;
-
- phyloTree->addSeqToTree(name, taxInfo);
-
- m->gobble(inTax);
- }
- inTax.close();
-#endif
-
- phyloTree->assignHeirarchyIDs(0);
-
- phyloTree->setUp(file);
-
- m->mothurOut("DONE.");
- m->mothurOutEndLine(); cout.flush();
-
- return phyloTree->getNumSeqs();
-
- }
- catch(exception& e) {
- m->errorOut(e, "Classify", "readTaxonomy");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-vector<string> Classify::parseTax(string tax) {
- try {
- vector<string> taxons;
-
- tax = tax.substr(0, tax.length()-1); //get rid of last ';'
-
- //parse taxonomy
- string individual;
- while (tax.find_first_of(';') != -1) {
- individual = tax.substr(0,tax.find_first_of(';'));
- tax = tax.substr(tax.find_first_of(';')+1, tax.length());
- taxons.push_back(individual);
-
- }
- //get last one
- taxons.push_back(tax);
-
- return taxons;
- }
- catch(exception& e) {
- m->errorOut(e, "Classify", "parseTax");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
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