added chimera.uchime

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 4f3047d4d3dcded81e738fba36a79abdc81e680b..70349e50f0264b68fba76c4f04ebbddd0c8c96f6 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -77,8 +77,15 @@ 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());
+               #endif
                system(blastCommand.c_str());
                
                ifstream m8FileHandle;
@@ -133,7 +140,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                        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 =  "\"" + 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());
                #endif
                
@@ -206,7 +213,7 @@ void BlastDB::generateDB() {
                #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;
+                       formatdbCommand = "\"" + path + "blast\\bin\\formatdb\" -p F -o T -i " + dbFileName;
                #endif
                system(formatdbCommand.c_str());                                                                //      to get the right sequence names, i think. -p F
                                                                                                                                        //      option tells formatdb that seqs are DNA, not prot