changed blastdb.cpp to no include sequence names in blast input filenames. modified...

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index b1a7b48d1108d747c1423eb0f8bad19e3ceede42..b995bd378a46d064ea36773e05bd9b0afe84fefa 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -67,7 +67,8 @@ 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();
@@ -80,18 +81,18 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                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());
+                       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+seq->getName()) + " -o " + blastFileName+seq->getName());
+                       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;
@@ -107,8 +108,8 @@ 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;
        }
@@ -127,8 +128,8 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                Scores.clear();
                
                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();
@@ -140,10 +141,10 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                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());
+                       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+seq->getName()) + " -o " + blastFileName+seq->getName());
+                       blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
                        //wrap entire string in ""
                        blastCommand = "\"" + blastCommand + "\"";
 
@@ -152,7 +153,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                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;
@@ -173,8 +174,8 @@ 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;
        }