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);
+ 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 + " -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);
+ m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
string dummy;
int templateAccession;
- gobble(m8FileHandle);
+ 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; } }
- gobble(m8FileHandle);
+ m->gobble(m8FileHandle);
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.
-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);
+ m->openOutputFile((queryFileName+seq->getName()), queryFile);
queryFile << '>' << seq->getName() << endl;
queryFile << seq->getUnaligned() << endl;
queryFile.close();
// 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);
- blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
+ 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, m8FileHandle);
+ m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
string dummy;
int templateAccession;
- gobble(m8FileHandle);
-//string name = seq->getName();
-//ofstream out;
-//openOutputFileAppend(name, out);
+ m->gobble(m8FileHandle);
+
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;
+ m->gobble(m8FileHandle);
+ topMatches.push_back(templateAccession);
+//cout << templateAccession << endl;
}
m8FileHandle.close();
-//out.close();
+ remove((queryFileName+seq->getName()).c_str());
+ remove((blastFileName+seq->getName()).c_str());
+//cout << "\n\n" ;
return topMatches;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "findClosest");
+ m->errorOut(e, "BlastDB", "findClosest");
exit(1);
}
}
try {
ofstream unalignedFastaFile;
- openOutputFileAppend(dbFileName, 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++;
}
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);
}
}
+/**************************************************************************************************/
/**************************************************************************************************/
projects / mothur.git / blobdiff