working on search=dist in chimera.slayer

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index aadff822bc9efb930f3a8f4c969fc3e5bc08e3fb..2d171391ca24ff1bfa43146de6ac5385de6ed46f 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";
 
 }
 /**************************************************************************************************/
@@ -123,11 +123,12 @@ 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());
                system(blastCommand.c_str());
@@ -141,7 +142,7 @@ 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' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
+                       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; }     } //
@@ -156,7 +157,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                m8FileHandle.close();
                remove((queryFileName+seq->getName()).c_str());
                remove((blastFileName+seq->getName()).c_str());
-//cout << "\n" ;               
+cout << "\n" ;         
                return topMatches;
        }
        catch(exception& e) {