/**************************************************************************************************/
-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) {
- globaldata = GlobalData::getInstance();
-
- cout << "Generating the temporary BLAST database...\t"; cout.flush();
+ 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);
-
- 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();
-
- 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
- cout << "DONE." << endl << endl; cout.flush();
- emptySequence = Sequence();
- emptySequence.setName("no_match");
- emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
- emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
-
+BlastDB::BlastDB() : Database() {
+ try {
+ count = 0;
+ int randNumber = rand();
+ dbFileName = toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = toString(randNumber) + ".blast";
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "BlastDB");
+ exit(1);
+ }
}
/**************************************************************************************************/
BlastDB::~BlastDB(){
- //for (int i = 0; i < templateSequences.size(); i++) { delete templateSequences[i]; }
- //templateSequences.clear();
- //delete emptySequence;
-
- remove(queryFileName.c_str()); // let's clean stuff up and remove the temp files
- 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
+ try{
+ remove(queryFileName.c_str()); // let's clean stuff up and remove the temp files
+ remove(dbFileName.c_str()); // let's clean stuff up and remove the temp files
+ remove((dbFileName+".nsq").c_str()); // let's clean stuff up and remove the temp files
+ remove((dbFileName+".nsi").c_str()); // let's clean stuff up and remove the temp files
+ remove((dbFileName+".nsd").c_str()); // let's clean stuff up and remove the temp files
+ remove((dbFileName+".nin").c_str()); // let's clean stuff up and remove the temp files
+ remove((dbFileName+".nhr").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
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "~BlastDB");
+ exit(1);
+ }
}
-
/**************************************************************************************************/
+//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;
+ m->openOutputFile((queryFileName+seq->getName()), 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+seq->getName()) + " -o " + blastFileName+seq->getName());
+ system(blastCommand.c_str());
+
+ ifstream m8FileHandle;
+ m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+
+ string dummy;
+ int templateAccession;
+ m->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; } }
+
+ m->gobble(m8FileHandle);
+ topMatches.push_back(templateAccession);
+ }
+ m8FileHandle.close();
+ remove((queryFileName+seq->getName()).c_str());
+ remove((blastFileName+seq->getName()).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;
+ Scores.clear();
+
+ ofstream queryFile;
+
+ m->openOutputFile((queryFileName+seq->getName()), 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.
-// 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+seq->getName()) + " -o " + blastFileName+seq->getName());
+ system(blastCommand.c_str());
- string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -b 1 -m 8 -W 28";
- blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
- system(blastCommand.c_str());
-
- ifstream m8FileHandle;
- openInputFile(blastFileName, m8FileHandle);
+ ifstream m8FileHandle;
+ m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
- string dummy;
- int templateAccession;
- gobble(m8FileHandle);
- if(!m8FileHandle.eof()){
- m8FileHandle >> dummy >> templateAccession >> searchScore;
+ string dummy;
+ int templateAccession;
+ m->gobble(m8FileHandle);
+
+ while(!m8FileHandle.eof()){
+ m8FileHandle >> dummy >> templateAccession >> searchScore;
+ //cout << templateAccession << '\t' << searchScore << endl;
+
+ //get rest of junk in line
+ while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; } }
+
+ m->gobble(m8FileHandle);
+ topMatches.push_back(templateAccession);
+ Scores.push_back(searchScore);
+//cout << templateAccession << endl;
+ }
m8FileHandle.close();
- return templateSequences[templateAccession];
+ remove((queryFileName+seq->getName()).c_str());
+ remove((blastFileName+seq->getName()).c_str());
+//cout << "\n" ;
+ return topMatches;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "findClosestMegaBlast");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void BlastDB::addSequence(Sequence seq) {
+ try {
+
+ ofstream unalignedFastaFile;
+ m->openOutputFileAppend(dbFileName, unalignedFastaFile);
+
+ // generating a fasta file with unaligned template
+ unalignedFastaFile << '>' << count << endl; // sequences, which will be input to formatdb
+ unalignedFastaFile << seq.getUnaligned() << endl;
+ unalignedFastaFile.close();
+
+ count++;
}
- else{
- searchScore = 0.00;
- return emptySequence;
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "addSequence");
+ exit(1);
}
- m8FileHandle.close();
}
+/**************************************************************************************************/
+void BlastDB::generateDB() {
+ try {
+
+ //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
+
+ path = m->argv;
+ string tempPath = path;
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.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();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "generateDB");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
/**************************************************************************************************/
+
projects / mothur.git / blobdiff