pat's updates on 7/19/10

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 2b46f2bcda9246b865759f832e070fbc27d8fe0d..69c34016e1c091b2f0a792b6ed990c82a0509fd7 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -74,7 +74,17 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
                                                if (pid == 0) {
                                        #endif
 
-                                       ableToOpen = openInputFile(fastaFileNames[i], in);
+                                       ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+                               
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getDefaultPath() != "") { //default path is set
+                                                       string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       fastaFileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        #ifdef USE_MPI  
@@ -89,7 +99,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
                                        #endif
 
                                        if (ableToOpen == 1) { 
-                                               m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
                                                //erase from file list
                                                fastaFileNames.erase(fastaFileNames.begin()+i);
                                                i--;
@@ -211,7 +221,6 @@ int ChimeraCcodeCommand::execute(){
                        }
 
                        string mapInfo = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "mapinfo";
-                       bool hasAccnos = true;
                        
                        if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); }  return 0;    }
                        
@@ -220,8 +229,7 @@ int ChimeraCcodeCommand::execute(){
                                int pid, end, numSeqsPerProcessor; 
                                int tag = 2001;
                                vector<long> MPIPos;
-                               MPIWroteAccnos = false;
-                               
+                                                               
                                MPI_Status status; 
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
                                MPI_Comm_size(MPI_COMM_WORLD, &processors); 
@@ -278,11 +286,6 @@ int ChimeraCcodeCommand::execute(){
                                        
                                        if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 
-                                       for (int i = 1; i < processors; i++) {
-                                               bool tempResult;
-                                               MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
-                                               if (tempResult != 0) { MPIWroteAccnos = true; }
-                                       }
                                }else{ //you are a child process
                                        MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPIPos.resize(numSeqs+1);
@@ -298,8 +301,6 @@ int ChimeraCcodeCommand::execute(){
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
                                        
                                        if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
-                                       
-                                       MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); 
                                }
                                
                                //close files 
@@ -308,14 +309,6 @@ int ChimeraCcodeCommand::execute(){
                                MPI_File_close(&outMPIAccnos);
                                
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-                               
-                               //delete accnos file if blank
-                               if (pid == 0) {
-                                       if (!MPIWroteAccnos) { 
-                                               hasAccnos = false;      
-                                               remove(accnosFileName.c_str()); 
-                                       }
-                               }
                                        
                #else
                        ofstream outHeader;
@@ -348,11 +341,8 @@ int ChimeraCcodeCommand::execute(){
                                                return 0;
                                        }
                                        
-                                       //delete accnos file if its blank 
-                                       if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
-                                                                       
                                }else{
-                                       vector<int> positions;
+                                       vector<unsigned long int> positions;
                                        processIDS.resize(0);
                                        
                                        ifstream inFASTA;
@@ -362,7 +352,7 @@ int ChimeraCcodeCommand::execute(){
                                        while(!inFASTA.eof()){
                                                input = getline(inFASTA);
                                                if (input.length() != 0) {
-                                                       if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
+                                                       if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
                                                }
                                        }
                                        inFASTA.close();
@@ -372,7 +362,7 @@ int ChimeraCcodeCommand::execute(){
                                        int numSeqsPerProcessor = numSeqs / processors;
                                        
                                        for (int i = 0; i < processors; i++) {
-                                               long int startPos = positions[ i * numSeqsPerProcessor ];
+                                               unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
                                                if(i == processors - 1){
                                                        numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
                                                }
@@ -383,6 +373,7 @@ int ChimeraCcodeCommand::execute(){
                                        createProcesses(outputFileName, fastaFileNames[s], accnosFileName); 
                                
                                        rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
+                                       rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
                                                
                                        //append output files
                                        for(int i=1;i<processors;i++){
@@ -390,24 +381,12 @@ int ChimeraCcodeCommand::execute(){
                                                remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
                                        }
                                        
-                                       vector<string> nonBlankAccnosFiles;
-                                       //delete blank accnos files generated with multiple processes
-                                       for(int i=0;i<processors;i++){  
-                                               if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
-                                                       nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
-                                               }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
+                                       //append output files
+                                       for(int i=1;i<processors;i++){
+                                               appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
+                                               remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
                                        }
                                        
-                                       //append accnos files
-                                       if (nonBlankAccnosFiles.size() != 0) { 
-                                               rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
-                                               
-                                               for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
-                                                       appendFiles(nonBlankAccnosFiles[h], accnosFileName);
-                                                       remove(nonBlankAccnosFiles[h].c_str());
-                                               }
-                                       }else{ hasAccnos = false;  }
-                                       
                                        if (m->control_pressed) { 
                                                remove(outputFileName.c_str()); 
                                                remove(accnosFileName.c_str());
@@ -438,8 +417,6 @@ int ChimeraCcodeCommand::execute(){
                                                return 0;
                                }
                                
-                               //delete accnos file if its blank 
-                               if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
                        #endif
        
                        appendFiles(outputFileName, tempHeader);
@@ -452,7 +429,7 @@ int ChimeraCcodeCommand::execute(){
                        
                        outputNames.push_back(outputFileName);
                        outputNames.push_back(mapInfo);
-                       if (hasAccnos) { outputNames.push_back(accnosFileName); }
+                       outputNames.push_back(accnosFileName); 
                        
                        for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                        
@@ -565,7 +542,6 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
                
                                        //print results
                                        bool isChimeric = chimera->print(outMPI, outAccMPI);
-                                       if (isChimeric) { MPIWroteAccnos = true;  }
                                }
                        }
                        delete candidateSeq;