changed blastdb.cpp to no include sequence names in blast input filenames. modified...

diff --git a/blastdb.cpp b/blastdb.cpp
index b1a7b48d1108d747c1423eb0f8bad19e3ceede42..b995bd378a46d064ea36773e05bd9b0afe84fefa 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -67,7 +67,8 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                vector<int> topMatches;
                
                ofstream queryFile;
-               m->openOutputFile((queryFileName+seq->getName()), queryFile);
+               int randNumber = rand();
+               m->openOutputFile((queryFileName+toString(randNumber)), queryFile);
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
@@ -80,18 +81,18 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                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());
+                       blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+                       blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
                #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());
+                       blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
                        //wrap entire string in ""
                        blastCommand = "\"" + blastCommand + "\"";
                #endif
                system(blastCommand.c_str());
                
                ifstream m8FileHandle;
-               m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+               m->openInputFile(blastFileName+toString(randNumber), m8FileHandle, "no error");
                
                string dummy;
                int templateAccession;
@@ -107,8 +108,8 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                        topMatches.push_back(templateAccession);
                }
                m8FileHandle.close();
-               remove((queryFileName+seq->getName()).c_str());
-               remove((blastFileName+seq->getName()).c_str());
+               remove((queryFileName+toString(randNumber)).c_str());
+               remove((blastFileName+toString(randNumber)).c_str());
 
                return topMatches;
        }
@@ -127,8 +128,8 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                Scores.clear();
                
                ofstream queryFile;
-
-               m->openOutputFile((queryFileName+seq->getName()), queryFile);
+               int randNumber = rand();
+               m->openOutputFile((queryFileName+toString(randNumber)), queryFile);
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
@@ -140,10 +141,10 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                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());
+                       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+seq->getName()) + " -o " + blastFileName+seq->getName());
+                       blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
                        //wrap entire string in ""
                        blastCommand = "\"" + blastCommand + "\"";
 
@@ -152,7 +153,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                system(blastCommand.c_str());
 
                ifstream m8FileHandle;
-               m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+               m->openInputFile(blastFileName+toString(randNumber), m8FileHandle, "no error");
        
                string dummy, eScore;
                int templateAccession;
@@ -173,8 +174,8 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 //cout << templateAccession << endl;
                }
                m8FileHandle.close();
-               remove((queryFileName+seq->getName()).c_str());
-               remove((blastFileName+seq->getName()).c_str());
+               remove((queryFileName+toString(randNumber)).c_str());
+               remove((blastFileName+toString(randNumber)).c_str());
 //cout << "\n" ;               
                return topMatches;
        }

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index bf502abe715baadd43112377c374ba218414d3d8..8e8c7b67715ae9fb262fe4a41f7c9ef121dc2bff 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -154,13 +154,8 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        
                        //check for required parameters
                        groupfile = validParameter.validFile(parameters, "group", true);
-                       if (groupfile == "not open") { abort = true; }
-                       else if (groupfile == "not found") { 
-                               //if there is a current design file, use it
-                               groupfile = m->getGroupFile(); 
-                               if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
-                               else {  m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }                                                             
-                       }
+                       if (groupfile == "not open") { groupfile = ""; abort = true; }
+                       else if (groupfile == "not found") { groupfile = ""; }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
@@ -217,9 +212,16 @@ int PhyloDiversityCommand::execute(){
                
                m->setTreeFile(treefile);
                
-               //read in group map info.
-               tmap = new TreeMap(groupfile);
-               tmap->readMap();
+               if (groupfile != "") {
+                       //read in group map info.
+                       tmap = new TreeMap(groupfile);
+                       tmap->readMap();
+               }else{ //fake out by putting everyone in one group
+                       Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
+                       tmap = new TreeMap();
+                       
+                       for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+               }
                
                if (namefile != "") { readNamesFile(); }
                
@@ -273,7 +275,7 @@ int PhyloDiversityCommand::execute(){
                }
                
                SharedUtil* util = new SharedUtil();
-               util->setGroups(m->Groups, tmap->namesOfGroups, "treegroup");   //sets the groups the user wants to analyze
+               util->setGroups(m->Groups, tmap->namesOfGroups, "phylo.diversity");     //sets the groups the user wants to analyze
                delete util;
                
                //incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed