X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastdb.cpp;h=b1a7b48d1108d747c1423eb0f8bad19e3ceede42;hb=1e8d08e96f4fe99604a6b3502568de464bf60891;hp=2d171391ca24ff1bfa43146de6ac5385de6ed46f;hpb=257f86c2d7b91c2530b7fc98c781d97f250a2a97;p=mothur.git

diff --git a/blastdb.cpp b/blastdb.cpp
index 2d17139..b1a7b48 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -77,8 +77,17 @@ 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+seq->getName()) + " -o " + blastFileName+seq->getName());
+		#else
+			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());
+			//wrap entire string in ""
+			blastCommand = "\"" + blastCommand + "\"";
+		#endif
 		system(blastCommand.c_str());
 		
 		ifstream m8FileHandle;
@@ -123,14 +132,23 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 		queryFile << '>' << seq->getName() << endl;
 		queryFile << seq->getUnaligned() << endl;
 		queryFile.close();
-		cout << seq->getUnaligned() << endl;
+//		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;
+		#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+seq->getName()) + " -o " + blastFileName+seq->getName());
+		#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+seq->getName()) + " -o " + blastFileName+seq->getName());
+			//wrap entire string in ""
+			blastCommand = "\"" + blastCommand + "\"";
+
+		#endif
 		
-		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;
@@ -142,7 +160,7 @@ 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; }	} //
@@ -157,7 +175,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 		m8FileHandle.close();
 		remove((queryFileName+seq->getName()).c_str());
 		remove((blastFileName+seq->getName()).c_str());
-cout << "\n" ;		
+//cout << "\n" ;		
 		return topMatches;
 	}
 	catch(exception& e) {
@@ -195,7 +213,15 @@ 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 + "\"";
+			//wrap entire string in ""
+			formatdbCommand = "\"" + formatdbCommand + "\"";
+		#endif
 		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();