X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastdb.cpp;h=35a19f485816c87db85b71c74ca138f00595b180;hb=725a3d4ff2442c79bfde0a75ed3e0904edcf03b7;hp=6b45a48ce379168e82300209a7668c3e07e4d0ab;hpb=63e089e0b3aad1741bab60119ed7ccc784dce347;p=mothur.git

diff --git a/blastdb.cpp b/blastdb.cpp
index 6b45a48..35a19f4 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -25,6 +25,19 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
 	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";
+
 }
 
 /**************************************************************************************************/
@@ -50,7 +63,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 		//	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());
 		
@@ -75,12 +88,58 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 		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, 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 + " -o " + blastFileName);
+		system(blastCommand.c_str());
+		
+		ifstream m8FileHandle;
+		openInputFile(blastFileName, 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();
+//cout << "\n\n" ;		
+		return topMatches;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "BlastDB", "findClosest");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
 void BlastDB::addSequence(Sequence seq) {
 	try {
 	
@@ -91,11 +150,11 @@ void BlastDB::addSequence(Sequence seq) {
 		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);
 	}
 }
@@ -103,7 +162,7 @@ void BlastDB::addSequence(Sequence seq) {
 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')));
@@ -111,13 +170,14 @@ void BlastDB::generateDB() {
 		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);
 	}
 }
+/**************************************************************************************************/
 
 /**************************************************************************************************/