update .gitignore

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index af157203630c68bc8e8cfd0e09a2bcf846e4d33c..a77880e5865130732f4860c9cd50dc11c91af6ce 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -14,19 +14,19 @@
 
 /**************************************************************************************************/
 
-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());
-#endif
+               string pid = m->mothurGetpid(threadID);
                
+        if (m->debug) { m->mothurOut("[DEBUG]: tag = " + tag + "\t pid = " + pid + "\n"); }
+        
                dbFileName = tag + pid + toString(randNumber) + ".template.unaligned.fasta";
                queryFileName = tag + pid + toString(randNumber) + ".candidate.unaligned.fasta";
                blastFileName = tag + pid + toString(randNumber) + ".blast";
@@ -38,7 +38,7 @@ 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 +47,7 @@ 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 +60,7 @@ 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 +76,7 @@ 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 +96,12 @@ 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 +110,7 @@ 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\\";
@@ -117,17 +118,13 @@ BlastDB::BlastDB(string b) : Database() {
                }
                
                int randNumber = rand();
-               string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               pid +=  toString(getpid());
-#endif
-               
+               string pid = m->mothurGetpid(threadID);
                dbFileName = pid + toString(randNumber) + ".template.unaligned.fasta";
                queryFileName = pid + toString(randNumber) + ".candidate.unaligned.fasta";
                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 +139,7 @@ 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 +155,7 @@ 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 +203,7 @@ 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 +216,7 @@ 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 +267,7 @@ 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 +279,7 @@ 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 +353,7 @@ 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 +373,24 @@ 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);
+       }
+}
+/**************************************************************************************************/
 
 /**************************************************************************************************/