X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastdb.cpp;h=2eced7e14dc6fa42e0147747fc622bfa088250f7;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=af157203630c68bc8e8cfd0e09a2bcf846e4d33c;hpb=4e4d3cb3315fe25b40383c6f65cd6be23f58903d;p=mothur.git

diff --git a/blastdb.cpp b/blastdb.cpp
index af15720..2eced7e 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -14,19 +14,23 @@
 
 /**************************************************************************************************/
 
-BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM, string b) : Database(), 
+BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM, string b, int tid) : Database(), 
 gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 	try {
 		count = 0;
 		path = b;
+		threadID = tid;
 
 		int randNumber = rand();
 		//int randNumber = 12345;
 		string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-		pid +=  toString(getpid());
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+		pid += getpid();	
+#else
+		pid += toString(threadID);	
 #endif
 		
+		
 		dbFileName = tag + pid + toString(randNumber) + ".template.unaligned.fasta";
 		queryFileName = tag + pid + toString(randNumber) + ".candidate.unaligned.fasta";
 		blastFileName = tag + pid + toString(randNumber) + ".blast";
@@ -38,7 +42,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 			for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
 			path = path.substr(0, (tempPath.find_last_of('m')));
 			
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			path += "blast/bin/";	
 #else
 			path += "blast\\bin\\";
@@ -47,7 +51,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 		
 		
 		string formatdbCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		formatdbCommand = path + "formatdb";	//	format the database, -o option gives us the ability
 #else
 		formatdbCommand = path + "formatdb.exe";
@@ -60,7 +64,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 		if(ableToOpen == 1) {	m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
 		
 		string blastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		blastCommand = path + "blastall";	//	format the database, -o option gives us the ability
 #else
 		blastCommand = path + "blastall.exe";
@@ -76,7 +80,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 		
 		
 		string megablastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		megablastCommand = path + "megablast";	//	format the database, -o option gives us the ability
 #else
 		megablastCommand = path + "megablast.exe";
@@ -96,11 +100,12 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 }
 /**************************************************************************************************/
 
-BlastDB::BlastDB(string b) : Database() {
+BlastDB::BlastDB(string b, int tid) : Database() {
 	try {
 		count = 0;
 		
 		path = b;
+		threadID = tid;
 		
 		//make sure blast exists in the write place
 		if (path == "") {
@@ -109,7 +114,7 @@ BlastDB::BlastDB(string b) : Database() {
 			for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
 			path = path.substr(0, (tempPath.find_last_of('m')));
 			
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			path += "blast/bin/";	
 #else
 			path += "blast\\bin\\";
@@ -118,8 +123,10 @@ BlastDB::BlastDB(string b) : Database() {
 		
 		int randNumber = rand();
 		string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-		pid +=  toString(getpid());
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+		pid += getpid();	
+#else
+		pid += toString(threadID);	
 #endif
 		
 		dbFileName = pid + toString(randNumber) + ".template.unaligned.fasta";
@@ -127,7 +134,7 @@ BlastDB::BlastDB(string b) : Database() {
 		blastFileName = pid + toString(randNumber) + ".blast";
 		
 		string formatdbCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		formatdbCommand = path + "formatdb";	//	format the database, -o option gives us the ability
 #else
 		formatdbCommand = path + "formatdb.exe";
@@ -142,7 +149,7 @@ BlastDB::BlastDB(string b) : Database() {
 		if(ableToOpen == 1) {	m->mothurOut("[ERROR]: " +  formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
 		
 		string blastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		blastCommand = path + "blastall";	//	format the database, -o option gives us the ability
 #else
 		blastCommand = path + "blastall.exe";
@@ -158,7 +165,7 @@ BlastDB::BlastDB(string b) : Database() {
 		
 		
 		string megablastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		megablastCommand = path + "megablast";	//	format the database, -o option gives us the ability
 #else
 		megablastCommand = path + "megablast.exe";
@@ -206,10 +213,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 		
 		ofstream queryFile;
 		int randNumber = rand();
-		string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-		pid +=  toString(getpid());
-#endif
+		string pid = scrubName(seq->getName());
 		
 		m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
 		queryFile << '>' << seq->getName() << endl;
@@ -222,7 +226,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 		//	long.  With this setting, it seems comparable in speed to the suffix tree approach.
 		
 		string blastCommand;
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		
 			blastCommand = path + "blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
 			blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
@@ -273,10 +277,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 		
 		ofstream queryFile;
 		int randNumber = rand();
-		string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-		pid += toString(getpid());
-#endif
+		string pid = scrubName(seq->getName());
 		
 		m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
 		queryFile << '>' << seq->getName() << endl;
@@ -288,7 +289,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 		//	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)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			blastCommand = path + "megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
 			blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
 		#else
@@ -362,7 +363,7 @@ void BlastDB::generateDB() {
 			
 		string formatdbCommand;
 		
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			formatdbCommand = path + "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
@@ -382,6 +383,24 @@ void BlastDB::generateDB() {
 	}
 }
 /**************************************************************************************************/
+string BlastDB::scrubName(string seqName) {
+	try {
+		
+		string cleanName = "";
+		
+		for (int i = 0; i < seqName.length(); i++) {
+			if (isalnum(seqName[i])) { cleanName += seqName[i]; }
+			else { cleanName += "_";  }
+		}
+		
+		return cleanName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "BlastDB", "scrubName");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
 
 /**************************************************************************************************/