X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastdb.cpp;h=48ae1686a35aae2f1a19e980c8b057c827c40021;hb=4de093e3b92bdab1579565cb2873553412f6671e;hp=aadff822bc9efb930f3a8f4c969fc3e5bc08e3fb;hpb=a105be5e5d5bf89abd2f143bc68a1f6270aeddc7;p=mothur.git

diff --git a/blastdb.cpp b/blastdb.cpp
index aadff82..48ae168 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -14,15 +14,16 @@
 
 /**************************************************************************************************/
 
-BlastDB::BlastDB(float gO, float gE, float m, float mM) : Database(), 
+BlastDB::BlastDB(string tag, float gO, float gE, float m, float mM) : Database(), 
 gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
 	
 	count = 0;
 
 	int randNumber = rand();
-	dbFileName = toString(randNumber) + ".template.unaligned.fasta";
-	queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
-	blastFileName = toString(randNumber) + ".blast";
+	//int randNumber = 12345;
+	dbFileName = tag + toString(randNumber) + ".template.unaligned.fasta";
+	queryFileName = tag + toString(randNumber) + ".candidate.unaligned.fasta";
+	blastFileName = tag + toString(randNumber) + ".blast";
 
 }
 /**************************************************************************************************/
@@ -32,6 +33,7 @@ BlastDB::BlastDB() : Database() {
 		count = 0;
 
 		int randNumber = rand();
+		//int randNumber = 12345;
 		dbFileName = toString(randNumber) + ".template.unaligned.fasta";
 		queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
 		blastFileName = toString(randNumber) + ".blast";
@@ -67,7 +69,8 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 		vector<int> topMatches;
 		
 		ofstream queryFile;
-		m->openOutputFile((queryFileName+seq->getName()), queryFile);
+		int randNumber = rand();
+		m->openOutputFile((queryFileName+toString(randNumber)), queryFile);
 		queryFile << '>' << seq->getName() << endl;
 		queryFile << seq->getUnaligned() << endl;
 		queryFile.close();
@@ -77,12 +80,22 @@ 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 + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
-		blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+		string blastCommand;
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		
+			blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+			blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
+		#else
+			blastCommand =  "\"" + path + "blast\\bin\\blastall\" -p blastn -d " + "\"" + dbFileName + "\"" + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+			blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
+			//wrap entire string in ""
+			blastCommand = "\"" + blastCommand + "\"";
+		#endif
+		
 		system(blastCommand.c_str());
 		
 		ifstream m8FileHandle;
-		m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+		m->openInputFile(blastFileName+toString(randNumber), m8FileHandle, "no error");
 		
 		string dummy;
 		int templateAccession;
@@ -98,8 +111,8 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 			topMatches.push_back(templateAccession);
 		}
 		m8FileHandle.close();
-		remove((queryFileName+seq->getName()).c_str());
-		remove((blastFileName+seq->getName()).c_str());
+		remove((queryFileName+toString(randNumber)).c_str());
+		remove((blastFileName+toString(randNumber)).c_str());
 
 		return topMatches;
 	}
@@ -118,22 +131,36 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 		Scores.clear();
 		
 		ofstream queryFile;
-
-		m->openOutputFile((queryFileName+seq->getName()), queryFile);
+		int randNumber = rand();
+		//int randNumber = 12345;
+		m->openOutputFile((queryFileName+toString(randNumber)), queryFile);
 		queryFile << '>' << seq->getName() << endl;
 		queryFile << seq->getUnaligned() << endl;
 		queryFile.close();
-				
+//		cout << seq->getUnaligned() << endl;
 		//	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.
 //7000004128189528left	0	100		66	0	0	1	66	61	126	1e-31	 131	
-		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());
+		string blastCommand;
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			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+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
+		#else
+		//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+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
+
+			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+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
+			//wrap entire string in ""
+			blastCommand = "\"" + blastCommand + "\"";
+
+		#endif
+		//cout << blastCommand << endl;
 		system(blastCommand.c_str());
 
 		ifstream m8FileHandle;
-		m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+		m->openInputFile(blastFileName+toString(randNumber), m8FileHandle, "no error");
 	
 		string dummy, eScore;
 		int templateAccession;
@@ -141,7 +168,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 		
 		while(!m8FileHandle.eof()){
 			m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
-			//cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
+//			cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
 			
 			//get rest of junk in line
 			//while (!m8FileHandle.eof())	{	char c = m8FileHandle.get(); if (c == 10 || c == 13){	break;	}else{ cout << c; }	} //
@@ -154,8 +181,8 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 //cout << templateAccession << endl;
 		}
 		m8FileHandle.close();
-		remove((queryFileName+seq->getName()).c_str());
-		remove((blastFileName+seq->getName()).c_str());
+		remove((queryFileName+toString(randNumber)).c_str());
+		remove((blastFileName+toString(randNumber)).c_str());
 //cout << "\n" ;		
 		return topMatches;
 	}
@@ -194,7 +221,18 @@ void BlastDB::generateDB() {
 		for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
 		path = path.substr(0, (tempPath.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
+		string formatdbCommand;
+		
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;	//	format the database, -o option gives us the ability
+		#else
+			//formatdbCommand = path + "blast\\bin\\formatdb -p F -o T -i " + dbFileName;	//	format the database, -o option gives us the ability
+
+			formatdbCommand = "\"" + path + "blast\\bin\\formatdb\" -p F -o T -i " + "\"" +  dbFileName + "\"";
+			//wrap entire string in ""
+			formatdbCommand = "\"" + formatdbCommand + "\"";
+		#endif
+		//cout << formatdbCommand << endl;
 		system(formatdbCommand.c_str());								//	to get the right sequence names, i think. -p F
 																	//	option tells formatdb that seqs are DNA, not prot
 		//m->mothurOut("DONE."); m->mothurOutEndLine();	m->mothurOutEndLine(); cout.flush();