From: westcott <westcott>
Date: Fri, 20 May 2011 13:30:51 +0000 (+0000)
Subject: changed blastdb.cpp to no include sequence names in blast input filenames. modified... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=d154abda2a21879424002f28c50c6e0965865acf

changed blastdb.cpp to no include sequence names in blast input filenames. modified phylo.diversity to allow for no group file.
---

diff --git a/blastdb.cpp b/blastdb.cpp
index b1a7b48..b995bd3 100644
--- 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 bf502ab..8e8c7b6 100644
--- 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