*
*/
-using namespace std;
-
#include "database.hpp"
#include "sequence.hpp"
/**************************************************************************************************/
-BlastDB::BlastDB(string fastaFileName, float gO, float gE, float m, float mM) : Database(fastaFileName),
+BlastDB::BlastDB(float gO, float gE, float m, float mM) : Database(),
gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
-
- cout << "Generating the temporary BLAST database...\t"; cout.flush();
+
+ globaldata = GlobalData::getInstance();
+ count = 0;
int randNumber = rand();
dbFileName = toString(randNumber) + ".template.unaligned.fasta";
queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
blastFileName = toString(randNumber) + ".blast";
+}
+/**************************************************************************************************/
- ofstream unalignedFastaFile;
- openOutputFile(dbFileName, unalignedFastaFile);
+BlastDB::BlastDB() : Database() {
- for(int i=0;i<numSeqs;i++){ // generating a fasta file with unaligned template
- unalignedFastaFile << '>' << i << endl; // sequences, which will be input to formatdb
- unalignedFastaFile << templateSequences[i]->getUnaligned() << endl;
- }
- unalignedFastaFile.close();
-
- string formatdbCommand = "~/Pipeline/src/cpp/production/blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
- system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
- // option tells formatdb that seqs are DNA, not prot
- cout << "DONE." << endl << endl; cout.flush();
- emptySequence = new Sequence();
- emptySequence->setName("no_match");
- emptySequence->setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
- emptySequence->setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+ globaldata = GlobalData::getInstance();
+ count = 0;
+ int randNumber = rand();
+ dbFileName = toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = toString(randNumber) + ".blast";
}
remove(dbFileName.c_str()); // let's clean stuff up and remove the temp files
remove(blastFileName.c_str()); // let's clean stuff up and remove the temp files
}
-
/**************************************************************************************************/
+//assumes you have added all the template sequences using the addSequence function and run generateDB.
+vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
+ try{
+ vector<int> topMatches;
+
+ ofstream queryFile;
+ openOutputFile(queryFileName, queryFile);
+ queryFile << '>' << seq->getName() << endl;
+ queryFile << seq->getUnaligned() << endl;
+ queryFile.close();
+
+ // the goal here is to quickly survey the database to find the closest match. To do this we are using the default
+ // wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
+ // long. With this setting, it seems comparable in speed to the suffix tree approach.
+
+ string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
+ blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
+ system(blastCommand.c_str());
+
+ ifstream m8FileHandle;
+ openInputFile(blastFileName, m8FileHandle);
+
+ string dummy;
+ int templateAccession;
+ gobble(m8FileHandle);
+
+ while(!m8FileHandle.eof()){
+ m8FileHandle >> dummy >> templateAccession >> searchScore;
+
+ //get rest of junk in line
+ while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; } }
+
+ gobble(m8FileHandle);
+ topMatches.push_back(templateAccession);
+ }
+ m8FileHandle.close();
+
+ string root = dbFileName;
+ string temp = dbFileName + ".nsq";
+ remove(temp.c_str());
+ temp = dbFileName + ".nsi";
+ remove(temp.c_str());
+
+ temp = dbFileName + ".nsd";
+ remove(temp.c_str());
+
+ temp = dbFileName + ".nin";
+ remove(temp.c_str());
+
+ temp = dbFileName + ".nhr";
+ remove(temp.c_str());
+
-Sequence* BlastDB::findClosestSequence(Sequence* candidate){
+
+ return topMatches;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "findClosestSequences");
+ exit(1);
+ }
- ofstream queryFile;
- openOutputFile(queryFileName, queryFile);
- queryFile << '>' << candidate->getName() << endl;
- queryFile << candidate->getUnaligned() << endl;
- queryFile.close();
+}
+/**************************************************************************************************/
+//assumes you have added all the template sequences using the addSequence function and run generateDB.
+vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
+ try{
+ vector<int> topMatches;
+
+ ofstream queryFile;
+ openOutputFile(queryFileName, queryFile);
+ queryFile << '>' << seq->getName() << endl;
+ queryFile << seq->getUnaligned() << endl;
+ queryFile.close();
+
+ // the goal here is to quickly survey the database to find the closest match. To do this we are using the default
+ // wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
+ // long. With this setting, it seems comparable in speed to the suffix tree approach.
+ string blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
+ system(blastCommand.c_str());
+
+ ifstream m8FileHandle;
+ openInputFile(blastFileName, m8FileHandle, "no error");
-// the goal here is to quickly survey the database to find the closest match. To do this we are using the default
-// wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
-// long. With this setting, it seems comparable in speed to the suffix tree approach.
-
- string blastCommand = "~/Pipeline/src/cpp/production/blast/bin/blastall -p blastn -d " + dbFileName + " -b 1 -m 8 -W 28";
- blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
- system(blastCommand.c_str());
+ string dummy;
+ int templateAccession;
+ gobble(m8FileHandle);
+
+ while(!m8FileHandle.eof()){
+ m8FileHandle >> dummy >> templateAccession >> searchScore;
+
+ //get rest of junk in line
+ while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; } }
+
+ gobble(m8FileHandle);
+ topMatches.push_back(templateAccession);
+//cout << templateAccession << endl;
+ }
+ m8FileHandle.close();
+//cout << "\n\n" ;
+ return topMatches;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "findClosest");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void BlastDB::addSequence(Sequence seq) {
+ try {
- ifstream m8FileHandle;
- openInputFile(blastFileName, m8FileHandle);
+ ofstream unalignedFastaFile;
+ openOutputFileAppend(dbFileName, unalignedFastaFile);
- string dummy;
- int templateAccession;
- gobble(m8FileHandle);
- if(!m8FileHandle.eof()){
- m8FileHandle >> dummy >> templateAccession >> searchScore;
- m8FileHandle.close();
- return templateSequences[templateAccession];
+ // generating a fasta file with unaligned template
+ unalignedFastaFile << '>' << count << endl; // sequences, which will be input to formatdb
+ unalignedFastaFile << seq.getUnaligned() << endl;
+ unalignedFastaFile.close();
+
+ count++;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "addSequence");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void BlastDB::generateDB() {
+ try {
+
+ //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
+
+ path = globaldata->argv;
+ path = path.substr(0, (path.find_last_of('m')));
+
+ string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
+ // option tells formatdb that seqs are DNA, not prot
+ //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
}
- else{
- searchScore = 0.00;
- return emptySequence;
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "generateDB");
+ exit(1);
}
}
+#ifdef USE_MPI
+/**************************************************************************************************/
+int BlastDB::MPISend(int receiver) {
+ try {
+
+ //send gapOpen - float
+ MPI_Send(&gapOpen, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
+
+ //send gapExtend - float
+ MPI_Send(&gapExtend, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
+
+ //send match - float
+ MPI_Send(&match, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
+
+ //send mismatch - float
+ MPI_Send(&misMatch, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "MPISend");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int BlastDB::MPIRecv(int sender) {
+ try {
+ MPI_Status status;
+
+ //receive gapOpen - float
+ MPI_Recv(&gapOpen, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ //receive gapExtend - float
+ MPI_Recv(&gapExtend, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ //receive match - float
+ MPI_Recv(&match, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ //receive mismatch - float
+ MPI_Recv(&misMatch, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "MPIRecv");
+ exit(1);
+ }
+}
+#endif
+/**************************************************************************************************/
/**************************************************************************************************/
+