v 19.3

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index b995bd378a46d064ea36773e05bd9b0afe84fefa..48ae1686a35aae2f1a19e980c8b057c827c40021 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -20,6 +20,7 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        count = 0;
 
        int randNumber = rand();
+       //int randNumber = 12345;
        dbFileName = tag + toString(randNumber) + ".template.unaligned.fasta";
        queryFileName = tag + toString(randNumber) + ".candidate.unaligned.fasta";
        blastFileName = tag + toString(randNumber) + ".blast";
@@ -32,6 +33,7 @@ BlastDB::BlastDB() : Database() {
                count = 0;
 
                int randNumber = rand();
+               //int randNumber = 12345;
                dbFileName = toString(randNumber) + ".template.unaligned.fasta";
                queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
                blastFileName = toString(randNumber) + ".blast";
@@ -89,6 +91,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                        //wrap entire string in ""
                        blastCommand = "\"" + blastCommand + "\"";
                #endif
+               
                system(blastCommand.c_str());
                
                ifstream m8FileHandle;
@@ -129,6 +132,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                
                ofstream queryFile;
                int randNumber = rand();
+               //int randNumber = 12345;
                m->openOutputFile((queryFileName+toString(randNumber)), queryFile);
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
@@ -143,13 +147,16 @@ 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+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+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
+
                        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+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
                        //wrap entire string in ""
                        blastCommand = "\"" + blastCommand + "\"";
 
                #endif
-               
+               //cout << blastCommand << endl;
                system(blastCommand.c_str());
 
                ifstream m8FileHandle;
@@ -219,10 +226,13 @@ 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;   //      format the database, -o option gives us the ability
+
                        formatdbCommand = "\"" + path + "blast\\bin\\formatdb\" -p F -o T -i " + "\"" +  dbFileName + "\"";
                        //wrap entire string in ""
                        formatdbCommand = "\"" + formatdbCommand + "\"";
                #endif
+               //cout << formatdbCommand << endl;
                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();