added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 2db19735a8726e78269fbcce2a58521aa2205b19..557f17c6b85c7eb61865591ad3a8481ffa38ed38 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -22,6 +22,66 @@ Classify::Classify(string tfile, string tempFile, string method, int kmerSize, f
                
                int start = time(NULL);
                int numSeqs = 0;
+               
+               m->mothurOut("Generating search database...    "); cout.flush();
+#ifdef USE_MPI 
+                       int pid;
+                       vector<long> positions;
+               
+                       MPI_Status status; 
+                       MPI_File inMPI;
+                       MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+       
+                       char inFileName[tempFile.length()];
+                       strcpy(inFileName, tempFile.c_str());
+       
+                       MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
+       
+                       if (pid == 0) { //only one process needs to scan file
+                               positions = setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs
+
+                               //send file positions to all processes
+                               MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
+                               MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos     
+                       }else{
+                               MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+                               positions.resize(numSeqs);
+                               MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+                       }
+                       
+                       //create database
+                       if(method == "kmer")                    {       database = new KmerDB(tempFile, kmerSize);                      }
+                       else if(method == "suffix")             {       database = new SuffixDB(numSeqs);                                                               }
+                       else if(method == "blast")              {       database = new BlastDB(gapOpen, gapExtend, match, misMatch);    }
+                       else if(method == "distance")   {       database = new DistanceDB();    }
+                       else {
+                               m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();
+                               database = new KmerDB(tempFile, 8);
+                       }
+
+                       //read file 
+                       for(int i=0;i<numSeqs;i++){
+                               //read next sequence
+                               int length = positions[i+1] - positions[i];
+                               char buf4[length];
+                               MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
+                               
+                               string tempBuf = buf4;
+                               if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+                               
+                               istringstream iss (tempBuf,istringstream::in);
+                               
+                               Sequence temp(iss);  
+                               if (temp.getName() != "") {
+                                       names.push_back(temp.getName());
+                                       database->addSequence(temp);    
+                               }
+                       }
+                       
+                       database->generateDB();
+                       MPI_File_close(&inMPI);
+       #else
+               
                //need to know number of template seqs for suffixdb
                if (method == "suffix") {
                        ifstream inFASTA;
@@ -30,8 +90,6 @@ Classify::Classify(string tfile, string tempFile, string method, int kmerSize, f
                        inFASTA.close();
                }
 
-               m->mothurOut("Generating search database...    "); cout.flush();
-                               
                bool needToGenerate = true;
                string kmerDBName;
                if(method == "kmer")                    {       
@@ -81,7 +139,7 @@ Classify::Classify(string tfile, string tempFile, string method, int kmerSize, f
                        }
                        fastaFile.close();
                }
-               
+#endif         
                database->setNumSeqs(names.size());
                
                m->mothurOut("DONE."); m->mothurOutEndLine();
@@ -99,14 +157,58 @@ void Classify::readTaxonomy(string file) {
        try {
                
                phyloTree = new PhyloTree();
+               string name, taxInfo;
                
-               ifstream inTax;
-               openInputFile(file, inTax);
-       
                m->mothurOutEndLine();
                m->mothurOut("Reading in the " + file + " taxonomy...\t");      cout.flush();
+
+#ifdef USE_MPI 
+               int pid, num;
+               vector<long> positions;
                
-               string name, taxInfo;
+               MPI_Status status; 
+               MPI_File inMPI;
+               MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+               
+               char inFileName[file.length()];
+               strcpy(inFileName, file.c_str());
+               
+               MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
+               
+               if (pid == 0) {
+                       positions = setFilePosEachLine(file, num);
+                       
+                       //send file positions to all processes
+                       MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
+                       MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos 
+               }else{
+                       MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+                       positions.resize(num);
+                       MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+               }
+       
+               //read file 
+               for(int i=0;i<num;i++){
+                       //read next sequence
+                       int length = positions[i+1] - positions[i];
+                       char buf4[length];
+
+                       MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
+
+                       string tempBuf = buf4;
+                       if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+                       
+                       istringstream iss (tempBuf,istringstream::in);
+                       iss >> name >> taxInfo;
+                       taxonomy[name] = taxInfo;
+                       phyloTree->addSeqToTree(name, taxInfo);
+               }
+               
+               MPI_File_close(&inMPI);
+#else                          
+               ifstream inTax;
+               openInputFile(file, inTax);
+       
                //read template seqs and save
                while (!inTax.eof()) {
                        inTax >> name >> taxInfo;
@@ -117,10 +219,11 @@ void Classify::readTaxonomy(string file) {
                
                        gobble(inTax);
                }
-               
-               phyloTree->assignHeirarchyIDs(0);
                inTax.close();
+#endif 
        
+               phyloTree->assignHeirarchyIDs(0);
+               
                m->mothurOut("DONE.");
                m->mothurOutEndLine();  cout.flush();