working on citations

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index cc85989dad80dd1b0f85997b3428006b7d353c5c..4f3047d4d3dcded81e738fba36a79abdc81e680b 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -14,15 +14,15 @@
 
 /**************************************************************************************************/
 
-BlastDB::BlastDB(float gO, float gE, float m, float mM) : Database(), 
+BlastDB::BlastDB(string tag, float gO, float gE, float m, float mM) : Database(), 
 gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        
        count = 0;
 
        int randNumber = rand();
-       dbFileName = toString(randNumber) + ".template.unaligned.fasta";
-       queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
-       blastFileName = toString(randNumber) + ".blast";
+       dbFileName = tag + toString(randNumber) + ".template.unaligned.fasta";
+       queryFileName = tag + toString(randNumber) + ".candidate.unaligned.fasta";
+       blastFileName = tag + toString(randNumber) + ".blast";
 
 }
 /**************************************************************************************************/
@@ -123,13 +123,20 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
-                               
+//             cout << seq->getUnaligned() << endl;
                //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
                //      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 = 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());
+               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());
+               #endif
+               
                system(blastCommand.c_str());
 
                ifstream m8FileHandle;
@@ -141,13 +148,13 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
-                       //cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t';
+//                     cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
                        
                        //get rest of junk in line
                        //while (!m8FileHandle.eof())   {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }else{ cout << c; }     } //
                                //cout << endl;
                        m->gobble(m8FileHandle);
-                       if (searchScore >= minPerID) {
+                       if (searchScore >= minPerID) { 
                                topMatches.push_back(templateAccession);
                                Scores.push_back(searchScore);
                        }
@@ -194,7 +201,13 @@ 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;
+               #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();