fixed bug with trim.seqs allfiles=t

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index d227bc6a88cc8553181065680c7dc56fd1707a21..b1a7b48d1108d747c1423eb0f8bad19e3ceede42 100644 (file)
--- 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;
@@ -128,9 +137,18 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                //      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;
@@ -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();