queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
blastFileName = toString(randNumber) + ".blast";
+}
+/**************************************************************************************************/
+
+BlastDB::BlastDB() : Database() {
+
+ globaldata = GlobalData::getInstance();
+ count = 0;
+
+ int randNumber = rand();
+ dbFileName = toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = toString(randNumber) + ".blast";
+
}
/**************************************************************************************************/
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 + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
- blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
+ 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();
-
- 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());
-
+ remove((queryFileName+seq->getName()).c_str());
+ remove((blastFileName+seq->getName()).c_str());
-
return topMatches;
}
catch(exception& e) {
vector<int> topMatches;
ofstream queryFile;
- openOutputFile(queryFileName, queryFile);
+ openOutputFile((queryFileName+seq->getName()), queryFile);
queryFile << '>' << seq->getName() << endl;
queryFile << seq->getUnaligned() << endl;
queryFile.close();
// 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);
+ blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
system(blastCommand.c_str());
-
+
ifstream m8FileHandle;
- openInputFile(blastFileName, m8FileHandle, "no error");
+ openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
string dummy;
int templateAccession;
//cout << templateAccession << endl;
}
m8FileHandle.close();
+ remove((queryFileName+seq->getName()).c_str());
+ remove((blastFileName+seq->getName()).c_str());
//cout << "\n\n" ;
return topMatches;
}
unalignedFastaFile << '>' << count << endl; // sequences, which will be input to formatdb
unalignedFastaFile << seq.getUnaligned() << endl;
unalignedFastaFile.close();
-
+
count++;
}
catch(exception& e) {
exit(1);
}
}
+/**************************************************************************************************/
/**************************************************************************************************/