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/*
* alignmentdb.cpp
* Mothur
*
* Created by westcott on 11/4/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "alignmentdb.h"
#include "kmerdb.hpp"
#include "suffixdb.hpp"
#include "blastdb.hpp"
#include "referencedb.h"
/**************************************************************************************************/
AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid){ // This assumes that the template database is in fasta format, may
try { // need to alter this in the future?
m = MothurOut::getInstance();
longest = 0;
method = s;
bool needToGenerate = true;
ReferenceDB* rdb = ReferenceDB::getInstance();
bool silent = false;
threadID = tid;
if (fastaFileName == "saved-silent") {
fastaFileName = "saved"; silent = true;
}
if (fastaFileName == "saved") {
int start = time(NULL);
if (!silent) { m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine(); }
for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
templateSequences.push_back(rdb->referenceSeqs[i]);
//save longest base
if (rdb->referenceSeqs[i].getUnaligned().length() >= longest) { longest = (rdb->referenceSeqs[i].getUnaligned().length()+1); }
}
fastaFileName = rdb->getSavedReference();
numSeqs = templateSequences.size();
if (!silent) { m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine(); }
}else {
int start = time(NULL);
m->mothurOutEndLine();
m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
//bool aligned = false;
int tempLength = 0;
#ifdef USE_MPI
int pid, processors;
vector<unsigned long long> positions;
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);
int tag = 2001;
char inFileName[1024];
strcpy(inFileName, fastaFileName.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
if (pid == 0) {
positions = m->setFilePosFasta(fastaFileName, 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);
}
//read file
for(int i=0;i<numSeqs;i++){
if (m->control_pressed) { templateSequences.clear(); break; }
//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() != "") {
templateSequences.push_back(temp);
if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
//save longest base
if (temp.getUnaligned().length() >= longest) { longest = temp.getUnaligned().length()+1; }
if (tempLength != 0) {
if (tempLength != temp.getAligned().length()) { m->mothurOut("[ERROR]: template is not aligned, aborting.\n"); m->control_pressed=true; }
}else { tempLength = temp.getAligned().length(); }
}
}
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
MPI_File_close(&inMPI);
#else
ifstream fastaFile;
m->openInputFile(fastaFileName, fastaFile);
while (!fastaFile.eof()) {
Sequence temp(fastaFile); m->gobble(fastaFile);
if (m->control_pressed) { templateSequences.clear(); break; }
if (temp.getName() != "") {
templateSequences.push_back(temp);
if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
//save longest base
if (temp.getUnaligned().length() >= longest) { longest = (temp.getUnaligned().length()+1); }
if (tempLength != 0) {
if (tempLength != temp.getAligned().length()) { m->mothurOut("[ERROR]: template is not aligned, aborting.\n"); m->control_pressed=true; }
}else { tempLength = temp.getAligned().length(); }
}
}
fastaFile.close();
#endif
numSeqs = templateSequences.size();
//all of this is elsewhere already!
m->mothurOut("DONE.");
m->mothurOutEndLine(); cout.flush();
m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(templateSequences.size()) + " sequences."); m->mothurOutEndLine();
}
//in case you delete the seqs and then ask for them
emptySequence = Sequence();
emptySequence.setName("no_match");
emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
string kmerDBName;
if(method == "kmer") {
search = new KmerDB(fastaFileName, kmerSize);
#ifdef USE_MPI
#else
kmerDBName = fastaFileName.substr(0,fastaFileName.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; }
}
#endif
}
else if(method == "suffix") { search = new SuffixDB(numSeqs); }
else if(method == "blast") { search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID); }
else {
method = "kmer";
m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
m->mothurOutEndLine();
search = new KmerDB(fastaFileName, 8);
}
if (!(m->control_pressed)) {
if (needToGenerate) {
//add sequences to search
for (int i = 0; i < templateSequences.size(); i++) {
search->addSequence(templateSequences[i]);
if (m->control_pressed) { templateSequences.clear(); break; }
}
if (m->control_pressed) { templateSequences.clear(); }
search->generateDB();
}else if ((method == "kmer") && (!needToGenerate)) {
ifstream kmerFileTest(kmerDBName.c_str());
search->readKmerDB(kmerFileTest);
}
search->setNumSeqs(numSeqs);
}
}
catch(exception& e) {
m->errorOut(e, "AlignmentDB", "AlignmentDB");
exit(1);
}
}
/**************************************************************************************************/
AlignmentDB::AlignmentDB(string s){
try {
m = MothurOut::getInstance();
method = s;
if(method == "suffix") { search = new SuffixDB(); }
else if(method == "blast") { search = new BlastDB("", 0); }
else { search = new KmerDB(); }
//in case you delete the seqs and then ask for them
emptySequence = Sequence();
emptySequence.setName("no_match");
emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
}
catch(exception& e) {
m->errorOut(e, "AlignmentDB", "AlignmentDB");
exit(1);
}
}
/**************************************************************************************************/
AlignmentDB::~AlignmentDB() { delete search; }
/**************************************************************************************************/
Sequence AlignmentDB::findClosestSequence(Sequence* seq) {
try{
vector<int> spot = search->findClosestSequences(seq, 1);
if (spot.size() != 0) { return templateSequences[spot[0]]; }
else { return emptySequence; }
}
catch(exception& e) {
m->errorOut(e, "AlignmentDB", "findClosestSequence");
exit(1);
}
}
/**************************************************************************************************/
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