X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastdb.cpp;h=bc92e1c5f083831a88ec2d10e7a0fe94c68bb6b7;hb=a4f05f09c250323132a4b9427f41a3ededaec634;hp=17db069cdedb8a019d980c32fc4b6e7767fab27b;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/blastdb.cpp b/blastdb.cpp
index 17db069..bc92e1c 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -26,13 +26,41 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
 	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.
@@ -41,25 +69,26 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 		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 + " -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);
+		m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
 		
 		string dummy;
 		int templateAccession;
-		gobble(m8FileHandle);
+		m->gobble(m8FileHandle);
 		
 		while(!m8FileHandle.eof()){
 			m8FileHandle >> dummy >> templateAccession >> searchScore;
@@ -67,28 +96,13 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 			//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();
-		
-		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) {
@@ -104,7 +118,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
 		vector<int> topMatches;
 		
 		ofstream queryFile;
-		openOutputFile(queryFileName, queryFile);
+		m->openOutputFile((queryFileName+seq->getName()), queryFile);
 		queryFile << '>' << seq->getName() << endl;
 		queryFile << seq->getUnaligned() << endl;
 		queryFile.close();
@@ -114,27 +128,30 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
 		//	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");
+		m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
 	
 		string dummy;
 		int templateAccession;
-		gobble(m8FileHandle);
+		m->gobble(m8FileHandle);
 		
 		while(!m8FileHandle.eof()){
 			m8FileHandle >> dummy >> templateAccession >> searchScore;
+			//cout << templateAccession << '\t' << searchScore << endl;
 			
 			//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);
 //cout << templateAccession << endl;
 		}
 		m8FileHandle.close();
+		remove((queryFileName+seq->getName()).c_str());
+		remove((blastFileName+seq->getName()).c_str());
 //cout << "\n\n" ;		
 		return topMatches;
 	}
@@ -148,13 +165,13 @@ void BlastDB::addSequence(Sequence seq) {
 	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) {
@@ -181,6 +198,7 @@ void BlastDB::generateDB() {
 		exit(1);
 	}
 }
+/**************************************************************************************************/
 
 /**************************************************************************************************/