X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastdb.cpp;h=760824dbb23f9b2a9d680ace769ccc1c6ffab96c;hb=f07bf12e0d04340698aff7a36d2fee7c959ffe59;hp=396a6b4b91c4496b80dfc3009cdda4a0f34b12e6;hpb=81276c241b984898f8d30ad123c00592ee6db7b8;p=mothur.git

diff --git a/blastdb.cpp b/blastdb.cpp
index 396a6b4..760824d 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";
+
 }
 
 /**************************************************************************************************/
@@ -41,21 +54,22 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 		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;
@@ -71,28 +85,13 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 			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) {
-		errorOut(e, "BlastDB", "findClosestSequences");
+		m->errorOut(e, "BlastDB", "findClosestSequences");
 		exit(1);
 	}
 
@@ -104,7 +103,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
 		vector<int> topMatches;
 		
 		ofstream queryFile;
-		openOutputFile(queryFileName, queryFile);
+		openOutputFile((queryFileName+seq->getName()), queryFile);
 		queryFile << '>' << seq->getName() << endl;
 		queryFile << seq->getUnaligned() << endl;
 		queryFile.close();
@@ -114,11 +113,11 @@ 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");
+		openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
 	
 		string dummy;
 		int templateAccession;
@@ -135,11 +134,13 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
 //cout << templateAccession << endl;
 		}
 		m8FileHandle.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);
 	}
 }
@@ -154,11 +155,11 @@ 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);
 	}
 }
@@ -166,7 +167,7 @@ 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')));
@@ -174,13 +175,14 @@ 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);
 	}
 }
+/**************************************************************************************************/
 
 /**************************************************************************************************/