// 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);
+ 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());
}
/**************************************************************************************************/
//assumes you have added all the template sequences using the addSequence function and run generateDB.
-map<int, float> BlastDB::findClosest(Sequence* seq, int n) {
+vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
try{
- map<int, float> topMatches;
+ vector<int> topMatches;
ofstream queryFile;
openOutputFile(queryFileName, queryFile);
// 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 -b " + toString(n) + " -v " + toString(n);
+ 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());
string dummy;
int templateAccession;
gobble(m8FileHandle);
-//string name = seq->getName();
-//ofstream out;
-//openOutputFileAppend(name, out);
+
while(!m8FileHandle.eof()){
m8FileHandle >> dummy >> templateAccession >> searchScore;
-//out << dummy << '\t' << templateAccession << '\t' << searchScore << endl;
+
//get rest of junk in line
- while (!m8FileHandle.eof()) { char c = m8FileHandle.get();
- //out << c;
- if (c == 10 || c == 13){ break; } }
+ while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; } }
gobble(m8FileHandle);
- topMatches[templateAccession] = searchScore;
+ topMatches.push_back(templateAccession);
}
m8FileHandle.close();
-//out.close();
+
return topMatches;
}
catch(exception& e) {