blastFileName = toString(randNumber) + ".blast";
}
+/**************************************************************************************************/
+
+BlastDB::BlastDB() : Database() {
+ try {
+ globaldata = GlobalData::getInstance();
+ 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(){
- 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> topMatches;
ofstream queryFile;
- openOutputFile(queryFileName, queryFile);
+ 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 + " -b 1 -m 8 -W 28 -v " + toString(n);
- blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
+ 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;
- openInputFile(blastFileName, m8FileHandle);
+ openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
string dummy;
int templateAccession;
topMatches.push_back(templateAccession);
}
m8FileHandle.close();
-
+ remove((queryFileName+seq->getName()).c_str());
+ remove((blastFileName+seq->getName()).c_str());
+
return topMatches;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "findClosestSequences");
+ m->errorOut(e, "BlastDB", "findClosestSequences");
exit(1);
}
}
/**************************************************************************************************/
+//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+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/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());
+
+ ifstream m8FileHandle;
+ openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+
+ 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();
+ remove((queryFileName+seq->getName()).c_str());
+ remove((blastFileName+seq->getName()).c_str());
+//cout << "\n\n" ;
+ return topMatches;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "findClosest");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
void BlastDB::addSequence(Sequence seq) {
try {
unalignedFastaFile << '>' << count << endl; // sequences, which will be input to formatdb
unalignedFastaFile << seq.getUnaligned() << endl;
unalignedFastaFile.close();
-
+
count++;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "addSequence");
+ m->errorOut(e, "BlastDB", "addSequence");
exit(1);
}
}
void BlastDB::generateDB() {
try {
- mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
+ //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
- mothurOut("DONE."); mothurOutEndLine(); mothurOutEndLine(); cout.flush();
+ //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
}
catch(exception& e) {
- errorOut(e, "BlastDB", "generateDB");
+ m->errorOut(e, "BlastDB", "generateDB");
exit(1);
}
}
+/**************************************************************************************************/
/**************************************************************************************************/